Starting phenix.real_space_refine on Mon Sep 23 20:34:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/09_2024/7yr7_34048.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/09_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_34048/09_2024/7yr7_34048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/09_2024/7yr7_34048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/09_2024/7yr7_34048.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/09_2024/7yr7_34048.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.92, per 1000 atoms: 0.77 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 338.2 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: 1.98 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: 1.20 Time building geometry restraints manager: 1.53 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: 0.00 - 2.09: 7187 2.09 - 4.18: 619 4.18 - 6.27: 86 6.27 - 8.36: 14 8.36 - 10.45: 6 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 3.040 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 3.040 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 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.250 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.250 ------------------------------------------------------------------------------- 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 : 0.403 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: 0.2420 time to fit residues: 32.5740 Evaluate side-chains 91 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 D 35 ASN D 52 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5421 Z= 0.180 Angle : 0.688 7.438 7912 Z= 0.357 Chirality : 0.043 0.215 1020 Planarity : 0.005 0.044 561 Dihedral : 25.766 168.863 2227 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.98 % Favored : 83.02 % Rotamer: Outliers : 5.11 % Allowed : 21.53 % Favored : 73.36 % 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: -4.52 (0.39), residues: 318 helix: -2.94 (0.52), residues: 55 sheet: -3.90 (0.78), residues: 20 loop : -3.22 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 43 TYR 0.010 0.002 TYR E 48 ARG 0.004 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: 14 poor density : 94 time to evaluate : 0.401 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: 0.7704 (mtt180) cc_final: 0.7422 (mtt180) REVERT: E 55 LYS cc_start: 0.7703 (mttt) cc_final: 0.7226 (mttt) REVERT: B 7 ARG cc_start: 0.6919 (ptp90) cc_final: 0.6359 (ttm170) REVERT: B 13 MET cc_start: 0.3265 (ttt) cc_final: 0.1750 (tmm) REVERT: B 31 ARG cc_start: 0.7661 (ttt180) cc_final: 0.6924 (mtp180) REVERT: C 35 ASN cc_start: 0.7832 (t0) cc_final: 0.7373 (m-40) outliers start: 14 outliers final: 9 residues processed: 103 average time/residue: 0.2289 time to fit residues: 28.2276 Evaluate side-chains 95 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.0040 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 29 GLN B 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5421 Z= 0.221 Angle : 0.692 7.890 7912 Z= 0.358 Chirality : 0.042 0.188 1020 Planarity : 0.005 0.035 561 Dihedral : 25.829 171.270 2222 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.87 % Favored : 81.13 % Rotamer: Outliers : 6.57 % Allowed : 24.82 % Favored : 68.61 % 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: -3.86 (0.43), residues: 318 helix: -1.98 (0.57), residues: 55 sheet: -4.04 (0.84), residues: 20 loop : -2.81 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.003 HIS B 43 TYR 0.015 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 117 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.469 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: E 55 LYS cc_start: 0.7616 (mttt) cc_final: 0.7102 (mttt) REVERT: G 31 ARG cc_start: 0.6991 (mtp180) cc_final: 0.6655 (mtp180) REVERT: B 7 ARG cc_start: 0.6916 (ptp90) cc_final: 0.6324 (ttm170) REVERT: B 13 MET cc_start: 0.3288 (ttt) cc_final: 0.1912 (tmm) REVERT: B 31 ARG cc_start: 0.7565 (ttt180) cc_final: 0.7308 (mtp180) REVERT: B 49 GLN cc_start: 0.7673 (tp40) cc_final: 0.7411 (tp40) REVERT: C 35 ASN cc_start: 0.7924 (t0) cc_final: 0.7439 (m-40) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 0.2215 time to fit residues: 29.2682 Evaluate side-chains 102 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain E residue 20 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 B residue 47 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 30 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 0.0970 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.0770 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 overall best weight: 1.1138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 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: 0.5992 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5421 Z= 0.151 Angle : 0.597 7.904 7912 Z= 0.303 Chirality : 0.039 0.154 1020 Planarity : 0.004 0.035 561 Dihedral : 25.533 176.929 2221 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.41 % Favored : 84.59 % Rotamer: Outliers : 4.74 % Allowed : 29.93 % 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: -3.30 (0.46), residues: 318 helix: -1.39 (0.62), residues: 55 sheet: -2.74 (1.07), residues: 20 loop : -2.55 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 43 TYR 0.008 0.001 TYR E 48 ARG 0.004 0.000 ARG B 44 *********************** 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 102 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 GLN cc_start: 0.8852 (mt0) cc_final: 0.8546 (mt0) REVERT: F 38 LYS cc_start: 0.5043 (mptt) cc_final: 0.4567 (mptt) REVERT: E 55 LYS cc_start: 0.7405 (mttt) cc_final: 0.6895 (mttt) REVERT: G 31 ARG cc_start: 0.6984 (mtp180) cc_final: 0.6669 (mtp180) REVERT: B 7 ARG cc_start: 0.6880 (ptp90) cc_final: 0.6259 (ttm170) REVERT: B 13 MET cc_start: 0.3360 (ttt) cc_final: 0.1956 (tmm) REVERT: B 31 ARG cc_start: 0.7621 (ttt180) cc_final: 0.7380 (mtp180) REVERT: B 49 GLN cc_start: 0.7743 (tp40) cc_final: 0.7528 (tp40) REVERT: C 1 MET cc_start: 0.6626 (ptm) cc_final: 0.5803 (ptp) REVERT: C 35 ASN cc_start: 0.7992 (t0) cc_final: 0.7535 (m-40) outliers start: 13 outliers final: 8 residues processed: 99 average time/residue: 0.2333 time to fit residues: 27.5530 Evaluate side-chains 92 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 23 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain D residue 14 VAL 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: 5.9990 chunk 29 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 0.0870 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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: 0.6195 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5421 Z= 0.328 Angle : 0.813 10.185 7912 Z= 0.413 Chirality : 0.046 0.175 1020 Planarity : 0.007 0.062 561 Dihedral : 26.155 166.074 2217 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.27 % Favored : 76.73 % Rotamer: Outliers : 6.93 % Allowed : 29.56 % Favored : 63.50 % 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: -3.68 (0.46), residues: 318 helix: -1.97 (0.61), residues: 55 sheet: -3.46 (1.14), residues: 20 loop : -2.69 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS C 43 TYR 0.021 0.002 TYR E 48 ARG 0.010 0.001 ARG E 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 112 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 GLU cc_start: 0.5376 (tp30) cc_final: 0.4914 (tp30) REVERT: F 29 GLN cc_start: 0.8790 (mt0) cc_final: 0.8549 (mt0) REVERT: E 1 MET cc_start: 0.6187 (ttm) cc_final: 0.5726 (ttm) REVERT: E 55 LYS cc_start: 0.7567 (mttt) cc_final: 0.7082 (mttt) REVERT: G 31 ARG cc_start: 0.7020 (mtp180) cc_final: 0.6680 (mtp180) REVERT: B 1 MET cc_start: 0.7378 (ptm) cc_final: 0.7108 (ptm) REVERT: B 7 ARG cc_start: 0.7016 (ptp90) cc_final: 0.6330 (ttt180) REVERT: B 31 ARG cc_start: 0.7561 (ttt180) cc_final: 0.7215 (mtp180) REVERT: B 49 GLN cc_start: 0.7753 (tp40) cc_final: 0.7508 (tp40) REVERT: C 1 MET cc_start: 0.6430 (ptm) cc_final: 0.6092 (ptp) REVERT: C 31 ARG cc_start: 0.7396 (mmt180) cc_final: 0.7152 (mmt-90) REVERT: C 35 ASN cc_start: 0.8043 (t0) cc_final: 0.7611 (m-40) outliers start: 19 outliers final: 16 residues processed: 105 average time/residue: 0.2167 time to fit residues: 27.6359 Evaluate side-chains 104 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 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 40 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 47 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 C residue 42 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain D residue 14 VAL 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: 2.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.4729 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= 0.273 Angle : 0.794 10.574 7912 Z= 0.394 Chirality : 0.045 0.169 1020 Planarity : 0.005 0.032 561 Dihedral : 26.058 166.907 2217 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.18 % Favored : 80.82 % Rotamer: Outliers : 8.03 % Allowed : 29.93 % Favored : 62.04 % 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: -3.47 (0.46), residues: 318 helix: -1.96 (0.60), residues: 55 sheet: None (None), residues: 0 loop : -2.65 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS E 43 TYR 0.017 0.002 TYR E 48 ARG 0.009 0.001 ARG E 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 109 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 GLN cc_start: 0.8841 (mt0) cc_final: 0.8601 (mt0) REVERT: F 31 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7055 (mtp85) REVERT: E 1 MET cc_start: 0.5853 (ttm) cc_final: 0.5285 (ttm) REVERT: E 55 LYS cc_start: 0.7478 (mttt) cc_final: 0.7016 (mttt) REVERT: G 31 ARG cc_start: 0.7067 (mtp180) cc_final: 0.6697 (mtp180) REVERT: B 1 MET cc_start: 0.7278 (ptm) cc_final: 0.7054 (ptm) REVERT: B 7 ARG cc_start: 0.6969 (ptp90) cc_final: 0.6364 (ttm170) REVERT: B 49 GLN cc_start: 0.7866 (tp40) cc_final: 0.7620 (tp40) REVERT: C 35 ASN cc_start: 0.8004 (t0) cc_final: 0.7571 (m-40) outliers start: 22 outliers final: 18 residues processed: 102 average time/residue: 0.2185 time to fit residues: 27.3332 Evaluate side-chains 102 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 32 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain B residue 14 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 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 44 ARG Chi-restraints excluded: chain D residue 14 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 overall best weight: 1.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 moved from start: 0.4924 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= 0.206 Angle : 0.699 9.245 7912 Z= 0.346 Chirality : 0.042 0.193 1020 Planarity : 0.004 0.028 561 Dihedral : 25.857 170.071 2217 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.87 % Favored : 81.13 % Rotamer: Outliers : 7.30 % Allowed : 31.02 % 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: -3.47 (0.46), residues: 318 helix: -1.76 (0.60), residues: 55 sheet: -2.83 (0.95), residues: 30 loop : -2.56 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 43 TYR 0.012 0.001 TYR E 48 ARG 0.007 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 104 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 GLN cc_start: 0.8869 (mt0) cc_final: 0.8644 (mt0) REVERT: E 1 MET cc_start: 0.5707 (ttm) cc_final: 0.4874 (ttm) REVERT: E 55 LYS cc_start: 0.7297 (mttt) cc_final: 0.6833 (mttt) REVERT: G 31 ARG cc_start: 0.7015 (mtp180) cc_final: 0.6642 (mtp180) REVERT: B 7 ARG cc_start: 0.7053 (ptp90) cc_final: 0.6227 (ttm-80) REVERT: C 35 ASN cc_start: 0.7926 (t0) cc_final: 0.7540 (m-40) outliers start: 20 outliers final: 14 residues processed: 99 average time/residue: 0.2384 time to fit residues: 29.3328 Evaluate side-chains 95 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 23 LEU 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 40 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain B residue 23 LEU 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 32 ILE Chi-restraints excluded: chain D residue 14 VAL 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: 2.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.6014 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5421 Z= 0.159 Angle : 0.631 8.605 7912 Z= 0.307 Chirality : 0.039 0.181 1020 Planarity : 0.004 0.050 561 Dihedral : 25.546 174.395 2217 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.41 % Favored : 84.59 % Rotamer: Outliers : 4.74 % Allowed : 33.21 % Favored : 62.04 % 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: -3.18 (0.45), residues: 318 helix: -1.52 (0.61), residues: 55 sheet: -2.41 (0.95), residues: 30 loop : -2.40 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 43 TYR 0.008 0.001 TYR E 48 ARG 0.006 0.001 ARG E 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 97 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 GLN cc_start: 0.8859 (mt0) cc_final: 0.8578 (mt0) REVERT: E 1 MET cc_start: 0.5647 (ttm) cc_final: 0.4662 (ttm) REVERT: E 44 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7280 (ptp-170) REVERT: E 55 LYS cc_start: 0.7165 (mttt) cc_final: 0.6703 (mttt) REVERT: B 7 ARG cc_start: 0.7001 (ptp90) cc_final: 0.6262 (ttm-80) REVERT: B 13 MET cc_start: 0.3764 (ttt) cc_final: 0.2553 (ttt) REVERT: C 35 ASN cc_start: 0.7961 (t0) cc_final: 0.7501 (m-40) outliers start: 13 outliers final: 8 residues processed: 95 average time/residue: 0.2347 time to fit residues: 27.2242 Evaluate side-chains 92 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 44 ARG Chi-restraints excluded: chain G residue 40 VAL 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 D residue 14 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 GLN ** 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: 0.5984 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5421 Z= 0.154 Angle : 0.635 10.084 7912 Z= 0.306 Chirality : 0.038 0.160 1020 Planarity : 0.005 0.092 561 Dihedral : 25.419 173.480 2217 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Rotamer: Outliers : 4.01 % Allowed : 34.31 % 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: -3.06 (0.45), residues: 318 helix: -1.43 (0.60), residues: 55 sheet: -2.28 (0.97), residues: 30 loop : -2.32 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 43 TYR 0.008 0.001 TYR E 48 ARG 0.009 0.001 ARG E 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 91 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 GLN cc_start: 0.8821 (mt0) cc_final: 0.8530 (mt0) REVERT: E 1 MET cc_start: 0.5700 (ttm) cc_final: 0.5065 (ttm) REVERT: E 55 LYS cc_start: 0.7154 (mttt) cc_final: 0.6696 (mttt) REVERT: B 1 MET cc_start: 0.7512 (ttt) cc_final: 0.6613 (ttp) REVERT: B 7 ARG cc_start: 0.6943 (ptp90) cc_final: 0.6229 (ttm170) REVERT: B 10 GLU cc_start: 0.5481 (mm-30) cc_final: 0.5174 (mm-30) REVERT: B 13 MET cc_start: 0.3638 (ttt) cc_final: 0.2480 (ttt) REVERT: C 35 ASN cc_start: 0.7957 (t0) cc_final: 0.7498 (m-40) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.2117 time to fit residues: 23.3607 Evaluate side-chains 88 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain B residue 25 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 D residue 14 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0030 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 0.3980 chunk 34 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 6 optimal weight: 6.9990 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.5869 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5421 Z= 0.147 Angle : 0.618 10.312 7912 Z= 0.297 Chirality : 0.037 0.169 1020 Planarity : 0.004 0.034 561 Dihedral : 25.165 176.966 2217 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 1.82 % Allowed : 36.50 % 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: -2.76 (0.46), residues: 318 helix: -1.07 (0.62), residues: 55 sheet: -2.37 (1.00), residues: 30 loop : -2.10 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 43 TYR 0.007 0.001 TYR C 48 ARG 0.006 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 88 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 29 GLN cc_start: 0.8769 (mt0) cc_final: 0.8489 (mt0) REVERT: E 1 MET cc_start: 0.5914 (ttm) cc_final: 0.4789 (ttm) REVERT: E 55 LYS cc_start: 0.7018 (mttt) cc_final: 0.6572 (mttt) REVERT: B 1 MET cc_start: 0.7596 (ttt) cc_final: 0.6956 (ttt) REVERT: B 7 ARG cc_start: 0.6862 (ptp90) cc_final: 0.6178 (ttm170) REVERT: B 10 GLU cc_start: 0.5404 (mm-30) cc_final: 0.5143 (mm-30) REVERT: B 13 MET cc_start: 0.3745 (ttt) cc_final: 0.2470 (ttt) REVERT: C 35 ASN cc_start: 0.7894 (t0) cc_final: 0.7389 (m-40) REVERT: D 10 GLU cc_start: 0.6388 (mm-30) cc_final: 0.5775 (mm-30) outliers start: 5 outliers final: 5 residues processed: 87 average time/residue: 0.2119 time to fit residues: 22.9127 Evaluate side-chains 83 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain D residue 14 VAL 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: 4.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.176339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.142476 restraints weight = 14143.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.145890 restraints weight = 8666.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.148225 restraints weight = 6204.567| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 5421 Z= 0.382 Angle : 0.901 11.043 7912 Z= 0.443 Chirality : 0.049 0.218 1020 Planarity : 0.007 0.071 561 Dihedral : 26.111 163.606 2217 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.01 % Favored : 77.99 % Rotamer: Outliers : 3.65 % Allowed : 37.23 % Favored : 59.12 % 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: -3.37 (0.46), residues: 318 helix: -2.01 (0.59), residues: 55 sheet: -5.53 (0.74), residues: 10 loop : -2.36 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 43 TYR 0.022 0.002 TYR E 48 ARG 0.010 0.001 ARG C 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1392.25 seconds wall clock time: 25 minutes 43.04 seconds (1543.04 seconds total)