Starting phenix.real_space_refine on Sun Mar 10 21:05:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/03_2024/7yr7_34048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/03_2024/7yr7_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_34048/03_2024/7yr7_34048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/03_2024/7yr7_34048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/03_2024/7yr7_34048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/03_2024/7yr7_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-dev-5265/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: 3.39, per 1000 atoms: 0.66 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: 2.40 Conformation dependent library (CDL) restraints added in 528.9 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: 1.76 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: 1.23 Time building geometry restraints manager: 2.56 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: 3003 34.32 - 68.63: 384 68.63 - 102.95: 55 102.95 - 137.27: 1 137.27 - 171.58: 2 Dihedral angle restraints: 3445 sinusoidal: 2517 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 3442 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: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.600 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.100 Find NCS groups from input model: 0.260 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.460 ------------------------------------------------------------------------------- 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 : 25.593 171.582 2847 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 : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 31 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7741 (mtt180) REVERT: E 55 LYS cc_start: 0.7684 (mttt) cc_final: 0.7199 (mttt) REVERT: B 7 ARG cc_start: 0.6979 (ptp90) cc_final: 0.6373 (ttm170) REVERT: B 31 ARG cc_start: 0.7764 (ttt180) cc_final: 0.7312 (mmm-85) REVERT: C 13 MET cc_start: 0.1168 (mtm) cc_final: 0.0761 (mpp) REVERT: C 42 VAL cc_start: 0.8757 (t) cc_final: 0.8528 (m) REVERT: D 10 GLU cc_start: 0.6359 (mm-30) cc_final: 0.5930 (mm-30) outliers start: 13 outliers final: 6 residues processed: 114 average time/residue: 0.2392 time to fit residues: 32.1985 Evaluate side-chains 91 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain D residue 44 ARG 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: 3.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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: 0.6039 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5421 Z= 0.206 Angle : 0.700 7.515 7912 Z= 0.362 Chirality : 0.043 0.225 1020 Planarity : 0.005 0.042 561 Dihedral : 25.955 177.964 2227 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 5.47 % Allowed : 22.26 % Favored : 72.26 % 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: -4.47 (0.40), residues: 318 helix: -2.71 (0.55), residues: 55 sheet: -3.96 (0.80), residues: 20 loop : -3.23 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 43 TYR 0.009 0.002 TYR E 48 ARG 0.004 0.001 ARG E 6 *********************** 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 111 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 31 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7571 (mtt180) REVERT: E 55 LYS cc_start: 0.7656 (mttt) cc_final: 0.7173 (mttt) REVERT: B 7 ARG cc_start: 0.6934 (ptp90) cc_final: 0.6398 (ttm170) REVERT: B 13 MET cc_start: 0.3370 (ttt) cc_final: 0.1887 (tmm) REVERT: B 31 ARG cc_start: 0.7644 (ttt180) cc_final: 0.6919 (mtp180) REVERT: B 49 GLN cc_start: 0.7631 (tp40) cc_final: 0.7119 (tp40) REVERT: C 35 ASN cc_start: 0.7867 (t0) cc_final: 0.7398 (m-40) outliers start: 15 outliers final: 11 residues processed: 105 average time/residue: 0.2468 time to fit residues: 30.8561 Evaluate side-chains 99 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 44 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 29 GLN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN C 28 ASN D 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 5421 Z= 0.457 Angle : 1.015 11.555 7912 Z= 0.521 Chirality : 0.054 0.255 1020 Planarity : 0.007 0.055 561 Dihedral : 26.747 171.010 2226 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 34.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.53 % Favored : 75.47 % Rotamer: Outliers : 11.68 % Allowed : 22.63 % Favored : 65.69 % 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: -4.46 (0.43), residues: 318 helix: -2.78 (0.53), residues: 53 sheet: -3.83 (1.08), residues: 20 loop : -3.21 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 43 TYR 0.024 0.003 TYR E 48 ARG 0.014 0.001 ARG D 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 130 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 98 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 GLU cc_start: 0.5835 (tp30) cc_final: 0.5270 (tp30) REVERT: E 1 MET cc_start: 0.7099 (ttm) cc_final: 0.6595 (ttm) REVERT: E 55 LYS cc_start: 0.7685 (mttt) cc_final: 0.7160 (mttt) REVERT: G 35 ASN cc_start: 0.4891 (OUTLIER) cc_final: 0.4281 (m110) REVERT: B 7 ARG cc_start: 0.7016 (ptp90) cc_final: 0.6342 (ttt180) REVERT: B 31 ARG cc_start: 0.7717 (ttt180) cc_final: 0.7253 (mtp180) REVERT: B 49 GLN cc_start: 0.7716 (tp40) cc_final: 0.7418 (tp40) REVERT: C 1 MET cc_start: 0.6866 (pmm) cc_final: 0.6594 (pmm) outliers start: 32 outliers final: 19 residues processed: 118 average time/residue: 0.2107 time to fit residues: 30.0493 Evaluate side-chains 115 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 29 GLN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5421 Z= 0.217 Angle : 0.712 8.868 7912 Z= 0.364 Chirality : 0.043 0.158 1020 Planarity : 0.004 0.033 561 Dihedral : 26.245 176.271 2222 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.55 % Favored : 81.45 % Rotamer: Outliers : 8.39 % Allowed : 25.91 % Favored : 65.69 % 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: -3.74 (0.45), residues: 318 helix: -2.23 (0.58), residues: 55 sheet: -2.93 (1.89), residues: 10 loop : -2.78 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 43 TYR 0.012 0.002 TYR E 48 ARG 0.005 0.001 ARG E 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 114 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 MET cc_start: 0.6792 (tmm) cc_final: 0.6197 (tmm) REVERT: F 29 GLN cc_start: 0.8749 (mt0) cc_final: 0.8549 (mt0) REVERT: E 1 MET cc_start: 0.6917 (ttm) cc_final: 0.6096 (ttm) REVERT: E 55 LYS cc_start: 0.7452 (mttt) cc_final: 0.6977 (mttt) REVERT: G 31 ARG cc_start: 0.6973 (mtp180) cc_final: 0.6696 (mtp180) REVERT: G 35 ASN cc_start: 0.4693 (OUTLIER) cc_final: 0.4159 (m-40) REVERT: G 46 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: B 7 ARG cc_start: 0.6934 (ptp90) cc_final: 0.6242 (ttt90) REVERT: B 49 GLN cc_start: 0.7691 (tp40) cc_final: 0.7360 (tp40) outliers start: 23 outliers final: 14 residues processed: 110 average time/residue: 0.2362 time to fit residues: 30.9675 Evaluate side-chains 102 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 44 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5421 Z= 0.248 Angle : 0.742 9.538 7912 Z= 0.376 Chirality : 0.043 0.152 1020 Planarity : 0.004 0.028 561 Dihedral : 26.268 172.656 2217 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.38 % Favored : 78.62 % Rotamer: Outliers : 8.76 % Allowed : 29.56 % Favored : 61.68 % 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: -3.66 (0.45), residues: 318 helix: -2.00 (0.62), residues: 55 sheet: -2.58 (1.99), residues: 10 loop : -2.78 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 43 TYR 0.015 0.002 TYR E 48 ARG 0.006 0.000 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 114 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 MET cc_start: 0.6609 (tmm) cc_final: 0.6096 (tmm) REVERT: E 1 MET cc_start: 0.6491 (ttm) cc_final: 0.5664 (ttm) REVERT: E 55 LYS cc_start: 0.7534 (mttt) cc_final: 0.7053 (mttt) REVERT: G 31 ARG cc_start: 0.7054 (mtp180) cc_final: 0.6739 (mtp180) REVERT: B 7 ARG cc_start: 0.6929 (ptp90) cc_final: 0.6216 (ttt180) REVERT: B 49 GLN cc_start: 0.7659 (tp40) cc_final: 0.7363 (tp40) REVERT: C 1 MET cc_start: 0.8313 (pmm) cc_final: 0.7881 (pmm) outliers start: 24 outliers final: 21 residues processed: 107 average time/residue: 0.2166 time to fit residues: 28.0415 Evaluate side-chains 108 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 44 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.0970 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 overall best weight: 2.0322 ------------------------------------------------------------------------------- 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN C 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5421 Z= 0.207 Angle : 0.689 9.270 7912 Z= 0.342 Chirality : 0.041 0.153 1020 Planarity : 0.004 0.029 561 Dihedral : 26.077 174.689 2217 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.81 % Favored : 80.19 % Rotamer: Outliers : 9.85 % Allowed : 28.83 % Favored : 61.31 % 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: -3.46 (0.45), residues: 318 helix: -1.72 (0.64), residues: 55 sheet: -2.39 (1.97), residues: 10 loop : -2.68 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS E 43 TYR 0.014 0.001 TYR E 48 ARG 0.003 0.000 ARG F 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 117 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 MET cc_start: 0.6553 (tmm) cc_final: 0.6129 (tmm) REVERT: F 29 GLN cc_start: 0.8785 (mt0) cc_final: 0.8369 (mt0) REVERT: E 1 MET cc_start: 0.6458 (ttm) cc_final: 0.6054 (ttm) REVERT: E 6 ARG cc_start: 0.7162 (mmt180) cc_final: 0.6251 (mmt180) REVERT: E 55 LYS cc_start: 0.7501 (mttt) cc_final: 0.7018 (mttt) REVERT: G 31 ARG cc_start: 0.7015 (mtp180) cc_final: 0.6651 (mtp180) REVERT: G 35 ASN cc_start: 0.4566 (OUTLIER) cc_final: 0.4216 (m-40) REVERT: G 46 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: B 7 ARG cc_start: 0.6985 (ptp90) cc_final: 0.6247 (ttt180) REVERT: B 49 GLN cc_start: 0.7678 (tp40) cc_final: 0.7373 (tp40) REVERT: C 1 MET cc_start: 0.8119 (pmm) cc_final: 0.7135 (pmm) outliers start: 27 outliers final: 22 residues processed: 112 average time/residue: 0.2113 time to fit residues: 28.7247 Evaluate side-chains 111 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 44 ARG 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: 9.9990 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5421 Z= 0.247 Angle : 0.736 9.861 7912 Z= 0.368 Chirality : 0.042 0.168 1020 Planarity : 0.005 0.032 561 Dihedral : 26.161 170.760 2217 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.64 % Favored : 77.36 % Rotamer: Outliers : 10.95 % Allowed : 30.29 % Favored : 58.76 % 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: -3.45 (0.46), residues: 318 helix: -1.80 (0.64), residues: 55 sheet: -2.30 (2.00), residues: 10 loop : -2.66 (0.40), residues: 253 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 G 6 *********************** 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 119 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 89 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 MET cc_start: 0.6567 (tmm) cc_final: 0.6121 (tmm) REVERT: F 29 GLN cc_start: 0.8834 (mt0) cc_final: 0.8531 (mt0) REVERT: E 1 MET cc_start: 0.6434 (ttm) cc_final: 0.5987 (ttm) REVERT: E 6 ARG cc_start: 0.7355 (mmt180) cc_final: 0.6342 (mmt180) REVERT: E 55 LYS cc_start: 0.7457 (mttt) cc_final: 0.6988 (mttt) REVERT: G 31 ARG cc_start: 0.7032 (mtp180) cc_final: 0.6664 (mtp180) REVERT: G 35 ASN cc_start: 0.4195 (OUTLIER) cc_final: 0.3802 (m-40) REVERT: B 7 ARG cc_start: 0.7057 (ptp90) cc_final: 0.6197 (ttt90) REVERT: B 49 GLN cc_start: 0.7717 (tp40) cc_final: 0.7394 (tp40) REVERT: C 1 MET cc_start: 0.8092 (pmm) cc_final: 0.7492 (pmm) REVERT: C 52 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8372 (pp30) outliers start: 30 outliers final: 26 residues processed: 112 average time/residue: 0.1841 time to fit residues: 25.5700 Evaluate side-chains 113 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 86 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 32 ILE 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: 0.2980 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** D 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5421 Z= 0.166 Angle : 0.645 8.782 7912 Z= 0.320 Chirality : 0.039 0.156 1020 Planarity : 0.004 0.029 561 Dihedral : 25.849 177.030 2217 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.72 % Favored : 84.28 % Rotamer: Outliers : 8.76 % Allowed : 31.75 % Favored : 59.49 % 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: -3.28 (0.46), residues: 318 helix: -1.61 (0.65), residues: 55 sheet: -2.50 (1.59), residues: 10 loop : -2.53 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS E 43 TYR 0.010 0.001 TYR E 48 ARG 0.010 0.001 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 109 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 GLN cc_start: 0.8813 (mt0) cc_final: 0.8409 (mt0) REVERT: F 31 ARG cc_start: 0.7617 (mtt180) cc_final: 0.6716 (mtp85) REVERT: E 1 MET cc_start: 0.6045 (ttm) cc_final: 0.5294 (ttm) REVERT: E 6 ARG cc_start: 0.7196 (mmt180) cc_final: 0.6273 (mmt180) REVERT: E 55 LYS cc_start: 0.7286 (mttt) cc_final: 0.6809 (mttt) REVERT: G 31 ARG cc_start: 0.6954 (mtp180) cc_final: 0.6600 (mtp180) REVERT: B 1 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.6871 (ttt) REVERT: B 7 ARG cc_start: 0.7057 (ptp90) cc_final: 0.6232 (ttm170) REVERT: C 1 MET cc_start: 0.7876 (pmm) cc_final: 0.7083 (pmm) outliers start: 24 outliers final: 17 residues processed: 103 average time/residue: 0.1931 time to fit residues: 24.6709 Evaluate side-chains 99 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 32 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5421 Z= 0.235 Angle : 0.719 9.367 7912 Z= 0.359 Chirality : 0.041 0.160 1020 Planarity : 0.005 0.033 561 Dihedral : 26.041 171.079 2217 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.33 % Favored : 77.67 % Rotamer: Outliers : 8.39 % Allowed : 33.21 % Favored : 58.39 % 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: -3.48 (0.46), residues: 318 helix: -1.68 (0.65), residues: 55 sheet: -3.05 (0.94), residues: 30 loop : -2.56 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS E 43 TYR 0.015 0.002 TYR E 48 ARG 0.011 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 110 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 GLN cc_start: 0.8827 (mt0) cc_final: 0.8552 (mt0) REVERT: F 31 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7230 (mtt180) REVERT: E 1 MET cc_start: 0.6434 (ttm) cc_final: 0.5894 (ttm) REVERT: E 55 LYS cc_start: 0.7498 (mttt) cc_final: 0.7032 (mttt) REVERT: G 31 ARG cc_start: 0.6957 (mtp180) cc_final: 0.6601 (mtp180) REVERT: B 1 MET cc_start: 0.7528 (ttt) cc_final: 0.7021 (ttt) REVERT: B 7 ARG cc_start: 0.7051 (ptp90) cc_final: 0.6253 (ttm170) REVERT: B 44 ARG cc_start: 0.6379 (OUTLIER) cc_final: 0.5472 (ttp-110) REVERT: B 49 GLN cc_start: 0.7656 (tp40) cc_final: 0.7402 (tp40) REVERT: C 1 MET cc_start: 0.7788 (pmm) cc_final: 0.6977 (pmm) outliers start: 23 outliers final: 22 residues processed: 104 average time/residue: 0.1975 time to fit residues: 25.3021 Evaluate side-chains 105 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 32 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5421 Z= 0.229 Angle : 0.727 9.720 7912 Z= 0.363 Chirality : 0.041 0.157 1020 Planarity : 0.005 0.045 561 Dihedral : 26.011 170.935 2217 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.44 % Favored : 79.56 % Rotamer: Outliers : 8.76 % Allowed : 32.48 % Favored : 58.76 % 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: -3.27 (0.46), residues: 318 helix: -1.87 (0.61), residues: 55 sheet: -2.32 (1.97), residues: 10 loop : -2.46 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS E 43 TYR 0.015 0.001 TYR E 48 ARG 0.010 0.001 ARG G 6 ********************** 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 109 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 GLN cc_start: 0.8821 (mt0) cc_final: 0.8598 (mt0) REVERT: F 31 ARG cc_start: 0.7679 (mtt180) cc_final: 0.6769 (mtp85) REVERT: E 1 MET cc_start: 0.5942 (ttm) cc_final: 0.5170 (ttm) REVERT: E 55 LYS cc_start: 0.7431 (mttt) cc_final: 0.6962 (mttt) REVERT: G 31 ARG cc_start: 0.6962 (mtp180) cc_final: 0.6589 (mtp180) REVERT: B 1 MET cc_start: 0.7512 (ttt) cc_final: 0.7142 (ttt) REVERT: B 7 ARG cc_start: 0.7074 (ptp90) cc_final: 0.6292 (ttm170) REVERT: B 44 ARG cc_start: 0.6343 (OUTLIER) cc_final: 0.5410 (ttp-110) REVERT: B 49 GLN cc_start: 0.7631 (tp40) cc_final: 0.7413 (tp40) REVERT: C 1 MET cc_start: 0.7645 (pmm) cc_final: 0.6913 (pmm) REVERT: C 52 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8356 (pp30) outliers start: 24 outliers final: 20 residues processed: 104 average time/residue: 0.2002 time to fit residues: 25.3530 Evaluate side-chains 104 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 32 ILE 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: 0.5980 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- 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 ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4409 r_free = 0.4409 target = 0.175273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.139996 restraints weight = 13727.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.143532 restraints weight = 8388.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.146048 restraints weight = 6012.783| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5421 Z= 0.243 Angle : 0.747 9.682 7912 Z= 0.372 Chirality : 0.042 0.165 1020 Planarity : 0.005 0.046 561 Dihedral : 26.025 168.309 2217 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.96 % Favored : 77.04 % Rotamer: Outliers : 8.39 % Allowed : 33.58 % Favored : 58.03 % 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: -3.48 (0.45), residues: 318 helix: -1.69 (0.64), residues: 55 sheet: -3.53 (1.15), residues: 20 loop : -2.57 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.003 HIS E 43 TYR 0.017 0.002 TYR E 48 ARG 0.010 0.001 ARG E 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1318.55 seconds wall clock time: 24 minutes 27.51 seconds (1467.51 seconds total)