Starting phenix.real_space_refine on Sat Jan 20 18:30:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfe_13373/01_2024/7pfe_13373.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfe_13373/01_2024/7pfe_13373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfe_13373/01_2024/7pfe_13373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfe_13373/01_2024/7pfe_13373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfe_13373/01_2024/7pfe_13373.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfe_13373/01_2024/7pfe_13373.pdb" } resolution = 4.4 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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 354 5.49 5 S 10 5.16 5 C 7617 2.51 5 N 2601 2.21 5 O 3298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 61": "OE1" <-> "OE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d ASP 51": "OD1" <-> "OD2" Residue "d PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 71": "OE1" <-> "OE2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "e TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 24": "OD1" <-> "OD2" Residue "f GLU 53": "OE1" <-> "OE2" Residue "f GLU 63": "OE1" <-> "OE2" Residue "g GLU 91": "OE1" <-> "OE2" Residue "h PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 93": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13880 Number of models: 1 Model: "" Number of chains: 11 Chain: "a" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "b" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "c" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "d" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "f" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "g" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "h" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3645 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "I" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3612 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "u" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 7.27, per 1000 atoms: 0.52 Number of scatterers: 13880 At special positions: 0 Unit cell: (133.35, 132.3, 119.7, 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 10 16.00 P 354 15.00 O 3298 8.00 N 2601 7.00 C 7617 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: 8.36 Conformation dependent library (CDL) restraints added in 1.4 seconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 70.6% alpha, 3.1% beta 174 base pairs and 308 stacking pairs defined. Time for finding SS restraints: 7.46 Creating SS restraints... Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.783A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE a 78 " --> pdb=" O ILE a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 removed outlier: 3.716A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 removed outlier: 3.542A pdb=" N GLN b 27 " --> pdb=" O ASP b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 74 removed outlier: 4.607A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 Processing helix chain 'c' and resid 16 through 21 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.205A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.560A pdb=" N ASP c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 37 through 49 removed outlier: 3.889A pdb=" N VAL d 41 " --> pdb=" O TYR d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 removed outlier: 3.551A pdb=" N ILE d 94 " --> pdb=" O THR d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 123 Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 76 removed outlier: 3.531A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 4.193A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.547A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.249A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'g' and resid 112 through 116 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 104 through 124 removed outlier: 4.177A pdb=" N LYS h 108 " --> pdb=" O GLY h 104 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 51 removed outlier: 4.340A pdb=" N LEU u 42 " --> pdb=" O PRO u 38 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER u 50 " --> pdb=" O ALA u 46 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS u 51 " --> pdb=" O VAL u 47 " (cutoff:3.500A) Processing helix chain 'u' and resid 58 through 69 Processing helix chain 'u' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.743A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'b' and resid 96 through 98 removed outlier: 6.347A pdb=" N THR b 96 " --> pdb=" O THR g 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'c' and resid 101 through 102 removed outlier: 6.565A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.504A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.226A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'u' and resid 56 through 57 433 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 444 hydrogen bonds 888 hydrogen bond angles 0 basepair planarities 174 basepair parallelities 308 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 8.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3118 1.34 - 1.46: 5388 1.46 - 1.58: 5614 1.58 - 1.71: 706 1.71 - 1.83: 20 Bond restraints: 14846 Sorted by residual: bond pdb=" CG GLU c 61 " pdb=" CD GLU c 61 " ideal model delta sigma weight residual 1.516 1.453 0.063 2.50e-02 1.60e+03 6.27e+00 bond pdb=" C3' DG I 350 " pdb=" O3' DG I 350 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.30e+00 bond pdb=" CD GLU e 105 " pdb=" OE1 GLU e 105 " ideal model delta sigma weight residual 1.249 1.212 0.037 1.90e-02 2.77e+03 3.80e+00 bond pdb=" C LEU d 101 " pdb=" N LEU d 102 " ideal model delta sigma weight residual 1.327 1.282 0.045 2.31e-02 1.87e+03 3.75e+00 bond pdb=" CG GLU e 97 " pdb=" CD GLU e 97 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.60e+00 ... (remaining 14841 not shown) Histogram of bond angle deviations from ideal: 96.90 - 104.04: 1254 104.04 - 111.19: 7078 111.19 - 118.33: 4846 118.33 - 125.47: 7200 125.47 - 132.61: 1185 Bond angle restraints: 21563 Sorted by residual: angle pdb=" N GLU e 94 " pdb=" CA GLU e 94 " pdb=" CB GLU e 94 " ideal model delta sigma weight residual 110.28 118.56 -8.28 1.55e+00 4.16e-01 2.85e+01 angle pdb=" N GLU c 61 " pdb=" CA GLU c 61 " pdb=" CB GLU c 61 " ideal model delta sigma weight residual 110.16 117.60 -7.44 1.48e+00 4.57e-01 2.53e+01 angle pdb=" N GLU e 105 " pdb=" CA GLU e 105 " pdb=" CB GLU e 105 " ideal model delta sigma weight residual 110.28 118.04 -7.76 1.55e+00 4.16e-01 2.51e+01 angle pdb=" N GLU b 63 " pdb=" CA GLU b 63 " pdb=" CB GLU b 63 " ideal model delta sigma weight residual 110.22 117.49 -7.27 1.54e+00 4.22e-01 2.23e+01 angle pdb=" N GLU a 50 " pdb=" CA GLU a 50 " pdb=" CB GLU a 50 " ideal model delta sigma weight residual 110.28 117.59 -7.31 1.55e+00 4.16e-01 2.22e+01 ... (remaining 21558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6170 35.97 - 71.93: 1826 71.93 - 107.90: 25 107.90 - 143.86: 4 143.86 - 179.83: 2 Dihedral angle restraints: 8027 sinusoidal: 5596 harmonic: 2431 Sorted by residual: dihedral pdb=" CA GLU b 74 " pdb=" C GLU b 74 " pdb=" N HIS b 75 " pdb=" CA HIS b 75 " ideal model delta harmonic sigma weight residual 180.00 149.98 30.02 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ILE b 50 " pdb=" C ILE b 50 " pdb=" N TYR b 51 " pdb=" CA TYR b 51 " ideal model delta harmonic sigma weight residual -180.00 -157.25 -22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA LEU a 60 " pdb=" C LEU a 60 " pdb=" N LEU a 61 " pdb=" CA LEU a 61 " ideal model delta harmonic sigma weight residual -180.00 -159.63 -20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 8024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2074 0.065 - 0.129: 334 0.129 - 0.194: 37 0.194 - 0.259: 10 0.259 - 0.323: 1 Chirality restraints: 2456 Sorted by residual: chirality pdb=" CA PHE e 104 " pdb=" N PHE e 104 " pdb=" C PHE e 104 " pdb=" CB PHE e 104 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA GLU a 94 " pdb=" N GLU a 94 " pdb=" C GLU a 94 " pdb=" CB GLU a 94 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA GLU c 61 " pdb=" N GLU c 61 " pdb=" C GLU c 61 " pdb=" CB GLU c 61 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2453 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE a 104 " 0.018 2.00e-02 2.50e+03 2.09e-02 7.62e+00 pdb=" CG PHE a 104 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE a 104 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE a 104 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE a 104 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE a 104 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE a 104 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE c 79 " -0.044 5.00e-02 4.00e+02 6.60e-02 6.98e+00 pdb=" N PRO c 80 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO c 80 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO c 80 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG d 99 " 0.214 9.50e-02 1.11e+02 9.63e-02 6.87e+00 pdb=" NE ARG d 99 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG d 99 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG d 99 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG d 99 " 0.001 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3060 2.79 - 3.32: 12862 3.32 - 3.85: 30171 3.85 - 4.37: 33418 4.37 - 4.90: 45752 Nonbonded interactions: 125263 Sorted by model distance: nonbonded pdb=" O GLN e 93 " pdb=" OG SER e 96 " model vdw 2.264 2.440 nonbonded pdb=" OE2 GLU u 52 " pdb=" OG SER u 54 " model vdw 2.270 2.440 nonbonded pdb=" OG SER c 40 " pdb=" O ARG c 42 " model vdw 2.292 2.440 nonbonded pdb=" OG1 THR d 90 " pdb=" OE1 GLU d 93 " model vdw 2.306 2.440 nonbonded pdb=" NE2 HIS a 113 " pdb=" OD1 ASP e 123 " model vdw 2.312 2.520 ... (remaining 125258 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 'a' selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'f' } ncs_group { reference = chain 'c' selection = chain 'g' } ncs_group { reference = chain 'd' selection = chain 'h' } 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 6.200 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 48.840 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 14846 Z= 0.375 Angle : 0.936 9.632 21563 Z= 0.535 Chirality : 0.049 0.323 2456 Planarity : 0.008 0.096 1498 Dihedral : 29.754 179.829 6461 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.43 (0.26), residues: 825 helix: 0.09 (0.20), residues: 566 sheet: -2.08 (1.53), residues: 10 loop : -0.80 (0.32), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS b 75 PHE 0.048 0.003 PHE a 104 TYR 0.035 0.003 TYR f 72 ARG 0.019 0.001 ARG d 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9307 (mp0) cc_final: 0.9024 (mp0) REVERT: a 81 ASP cc_start: 0.8781 (t0) cc_final: 0.8267 (p0) REVERT: a 94 GLU cc_start: 0.9252 (mp0) cc_final: 0.8561 (mp0) REVERT: c 25 PHE cc_start: 0.8697 (m-80) cc_final: 0.8220 (m-80) REVERT: c 72 ASP cc_start: 0.9478 (m-30) cc_final: 0.9250 (m-30) REVERT: d 85 LYS cc_start: 0.9666 (mppt) cc_final: 0.9452 (mmtm) REVERT: d 106 LEU cc_start: 0.9478 (mt) cc_final: 0.9171 (mt) REVERT: d 113 GLU cc_start: 0.9130 (mp0) cc_final: 0.8823 (mp0) REVERT: e 50 GLU cc_start: 0.9653 (mp0) cc_final: 0.9279 (mp0) REVERT: e 54 TYR cc_start: 0.9479 (m-80) cc_final: 0.9277 (m-80) REVERT: e 90 MET cc_start: 0.9263 (tpt) cc_final: 0.8975 (tpt) REVERT: e 106 ASP cc_start: 0.9480 (m-30) cc_final: 0.9138 (m-30) REVERT: e 120 MET cc_start: 0.7446 (mtt) cc_final: 0.7003 (mtt) REVERT: e 124 ILE cc_start: 0.9539 (mt) cc_final: 0.9015 (mp) REVERT: f 44 LYS cc_start: 0.9248 (ttmt) cc_final: 0.8999 (ttmt) REVERT: f 85 ASP cc_start: 0.8626 (m-30) cc_final: 0.8339 (m-30) REVERT: g 36 LYS cc_start: 0.9016 (mppt) cc_final: 0.8758 (mmtm) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2853 time to fit residues: 65.1108 Evaluate side-chains 105 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 89 ASN d 84 ASN ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 14846 Z= 0.367 Angle : 0.704 9.539 21563 Z= 0.417 Chirality : 0.038 0.157 2456 Planarity : 0.005 0.058 1498 Dihedral : 32.685 176.331 4809 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.43 % Allowed : 5.77 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 825 helix: 1.03 (0.20), residues: 578 sheet: -1.95 (1.45), residues: 10 loop : -0.47 (0.35), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS a 39 PHE 0.014 0.002 PHE f 100 TYR 0.019 0.002 TYR h 40 ARG 0.005 0.001 ARG h 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.034 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: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9309 (mp0) cc_final: 0.8994 (mp0) REVERT: a 120 MET cc_start: 0.8730 (mpp) cc_final: 0.7979 (mpp) REVERT: d 62 MET cc_start: 0.8691 (mmp) cc_final: 0.8418 (mmp) REVERT: d 99 ARG cc_start: 0.9347 (mtp85) cc_final: 0.8828 (ttm110) REVERT: e 50 GLU cc_start: 0.9607 (mp0) cc_final: 0.9315 (mp0) REVERT: e 104 PHE cc_start: 0.9669 (m-10) cc_final: 0.9087 (m-80) REVERT: e 106 ASP cc_start: 0.9508 (m-30) cc_final: 0.9297 (m-30) REVERT: e 125 GLN cc_start: 0.9427 (mp10) cc_final: 0.9183 (mp10) REVERT: f 44 LYS cc_start: 0.9301 (ttmt) cc_final: 0.8861 (ttmt) REVERT: f 85 ASP cc_start: 0.8584 (m-30) cc_final: 0.8322 (m-30) REVERT: g 61 GLU cc_start: 0.9443 (tm-30) cc_final: 0.9043 (tm-30) REVERT: g 73 ASN cc_start: 0.9497 (t0) cc_final: 0.9247 (t0) outliers start: 3 outliers final: 1 residues processed: 127 average time/residue: 0.2582 time to fit residues: 48.0995 Evaluate side-chains 92 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 HIS c 94 ASN ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14846 Z= 0.232 Angle : 0.618 7.666 21563 Z= 0.368 Chirality : 0.035 0.140 2456 Planarity : 0.004 0.055 1498 Dihedral : 32.588 176.108 4809 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.43 % Allowed : 2.45 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.28), residues: 825 helix: 1.37 (0.21), residues: 584 sheet: -1.72 (1.54), residues: 10 loop : -0.45 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS a 39 PHE 0.008 0.001 PHE f 100 TYR 0.013 0.001 TYR h 40 ARG 0.005 0.000 ARG f 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.039 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9315 (mp0) cc_final: 0.9000 (mp0) REVERT: a 94 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.9073 (mm-30) REVERT: b 58 LEU cc_start: 0.9839 (tt) cc_final: 0.9609 (pp) REVERT: b 62 LEU cc_start: 0.9745 (mm) cc_final: 0.9497 (mt) REVERT: b 72 TYR cc_start: 0.9210 (m-80) cc_final: 0.8989 (m-80) REVERT: b 74 GLU cc_start: 0.9280 (pm20) cc_final: 0.8888 (pm20) REVERT: c 25 PHE cc_start: 0.8610 (m-80) cc_final: 0.8266 (m-80) REVERT: c 90 ASP cc_start: 0.8568 (t70) cc_final: 0.7874 (t0) REVERT: c 91 GLU cc_start: 0.8976 (mp0) cc_final: 0.8754 (mm-30) REVERT: c 94 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8663 (m110) REVERT: c 95 LYS cc_start: 0.9497 (ttmm) cc_final: 0.9022 (mppt) REVERT: d 85 LYS cc_start: 0.9680 (mppt) cc_final: 0.9413 (mmtm) REVERT: d 99 ARG cc_start: 0.9266 (mtp85) cc_final: 0.8773 (ttm110) REVERT: e 50 GLU cc_start: 0.9633 (mp0) cc_final: 0.9304 (mp0) REVERT: e 104 PHE cc_start: 0.9612 (m-10) cc_final: 0.9028 (m-80) REVERT: e 106 ASP cc_start: 0.9417 (m-30) cc_final: 0.9212 (m-30) REVERT: f 44 LYS cc_start: 0.9288 (ttmt) cc_final: 0.8848 (ttmt) REVERT: f 58 LEU cc_start: 0.9833 (tt) cc_final: 0.9553 (pp) REVERT: f 74 GLU cc_start: 0.9446 (pm20) cc_final: 0.9184 (pm20) REVERT: f 85 ASP cc_start: 0.8543 (m-30) cc_final: 0.8257 (m-30) REVERT: g 61 GLU cc_start: 0.9431 (tm-30) cc_final: 0.9010 (tm-30) outliers start: 3 outliers final: 1 residues processed: 148 average time/residue: 0.2798 time to fit residues: 58.9900 Evaluate side-chains 114 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 109 optimal weight: 0.0670 chunk 97 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 overall best weight: 3.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14846 Z= 0.290 Angle : 0.632 8.834 21563 Z= 0.375 Chirality : 0.035 0.157 2456 Planarity : 0.005 0.050 1498 Dihedral : 32.514 174.505 4809 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.29 % Allowed : 3.75 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.28), residues: 825 helix: 1.62 (0.21), residues: 570 sheet: -1.51 (1.76), residues: 10 loop : -0.35 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS a 39 PHE 0.012 0.001 PHE f 100 TYR 0.039 0.002 TYR b 88 ARG 0.008 0.001 ARG b 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 0.939 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: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9313 (mp0) cc_final: 0.9085 (mt-10) REVERT: a 104 PHE cc_start: 0.9470 (m-80) cc_final: 0.9106 (m-80) REVERT: a 106 ASP cc_start: 0.8957 (m-30) cc_final: 0.8683 (m-30) REVERT: a 108 ASN cc_start: 0.8957 (m-40) cc_final: 0.8603 (m110) REVERT: b 58 LEU cc_start: 0.9842 (tt) cc_final: 0.9526 (pp) REVERT: c 25 PHE cc_start: 0.8604 (m-80) cc_final: 0.8290 (m-80) REVERT: c 90 ASP cc_start: 0.8482 (t70) cc_final: 0.8041 (t0) REVERT: c 91 GLU cc_start: 0.9021 (mp0) cc_final: 0.8795 (mm-30) REVERT: c 95 LYS cc_start: 0.9441 (ttmm) cc_final: 0.8938 (mppt) REVERT: d 85 LYS cc_start: 0.9681 (mppt) cc_final: 0.9444 (mmtm) REVERT: d 99 ARG cc_start: 0.9254 (mtp85) cc_final: 0.8752 (ttm110) REVERT: e 90 MET cc_start: 0.8859 (tpt) cc_final: 0.8591 (tpt) REVERT: e 104 PHE cc_start: 0.9519 (m-10) cc_final: 0.8959 (m-80) REVERT: e 106 ASP cc_start: 0.9426 (m-30) cc_final: 0.8733 (m-30) REVERT: e 120 MET cc_start: 0.6845 (mtt) cc_final: 0.6430 (mtt) REVERT: f 58 LEU cc_start: 0.9832 (tt) cc_final: 0.9561 (pp) REVERT: f 72 TYR cc_start: 0.9569 (m-80) cc_final: 0.9363 (m-80) REVERT: f 74 GLU cc_start: 0.9333 (pm20) cc_final: 0.9046 (pm20) REVERT: f 84 MET cc_start: 0.8988 (mmm) cc_final: 0.8718 (mmm) REVERT: f 85 ASP cc_start: 0.8450 (m-30) cc_final: 0.8163 (m-30) REVERT: g 36 LYS cc_start: 0.8968 (mptt) cc_final: 0.8636 (mmtm) REVERT: g 61 GLU cc_start: 0.9435 (tm-30) cc_final: 0.8997 (tm-30) REVERT: h 52 THR cc_start: 0.8365 (m) cc_final: 0.7967 (p) outliers start: 2 outliers final: 0 residues processed: 142 average time/residue: 0.2834 time to fit residues: 57.7731 Evaluate side-chains 106 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14846 Z= 0.336 Angle : 0.660 9.780 21563 Z= 0.389 Chirality : 0.036 0.152 2456 Planarity : 0.004 0.038 1498 Dihedral : 32.758 176.815 4809 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.14 % Allowed : 2.02 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.28), residues: 825 helix: 1.37 (0.21), residues: 580 sheet: -1.57 (1.78), residues: 10 loop : -0.22 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS a 39 PHE 0.009 0.001 PHE d 65 TYR 0.040 0.003 TYR f 98 ARG 0.005 0.001 ARG c 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.035 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: symmetry clash REVERT: a 50 GLU cc_start: 0.9319 (mp0) cc_final: 0.9000 (mp0) REVERT: a 81 ASP cc_start: 0.9126 (t0) cc_final: 0.8394 (p0) REVERT: a 105 GLU cc_start: 0.9547 (mm-30) cc_final: 0.9209 (mm-30) REVERT: a 106 ASP cc_start: 0.9011 (m-30) cc_final: 0.8800 (m-30) REVERT: c 25 PHE cc_start: 0.8718 (m-80) cc_final: 0.8353 (m-80) REVERT: c 90 ASP cc_start: 0.8450 (t70) cc_final: 0.8031 (t0) REVERT: d 85 LYS cc_start: 0.9654 (mppt) cc_final: 0.9424 (mmtm) REVERT: d 99 ARG cc_start: 0.9245 (mtp85) cc_final: 0.8732 (ttm110) REVERT: e 50 GLU cc_start: 0.9652 (mp0) cc_final: 0.9295 (mp0) REVERT: e 90 MET cc_start: 0.8939 (tpt) cc_final: 0.8667 (tpt) REVERT: e 104 PHE cc_start: 0.9545 (m-10) cc_final: 0.8967 (m-80) REVERT: e 106 ASP cc_start: 0.9209 (m-30) cc_final: 0.8851 (m-30) REVERT: f 59 LYS cc_start: 0.9837 (ptmm) cc_final: 0.9616 (ptmm) REVERT: f 84 MET cc_start: 0.8999 (mmm) cc_final: 0.8775 (mmm) REVERT: f 85 ASP cc_start: 0.8314 (m-30) cc_final: 0.8055 (m-30) REVERT: f 92 ARG cc_start: 0.9289 (ttp80) cc_final: 0.9002 (ttp80) REVERT: g 36 LYS cc_start: 0.8987 (mptt) cc_final: 0.8670 (mmtm) REVERT: g 61 GLU cc_start: 0.9417 (tm-30) cc_final: 0.8964 (tm-30) REVERT: h 52 THR cc_start: 0.8399 (m) cc_final: 0.7983 (p) REVERT: h 71 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8611 (mm-30) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.3129 time to fit residues: 60.2801 Evaluate side-chains 99 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 90 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 HIS e 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14846 Z= 0.183 Angle : 0.602 7.334 21563 Z= 0.356 Chirality : 0.034 0.163 2456 Planarity : 0.004 0.053 1498 Dihedral : 32.362 177.872 4809 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.29 % Allowed : 2.02 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.28), residues: 825 helix: 1.71 (0.21), residues: 580 sheet: -1.66 (1.68), residues: 10 loop : -0.50 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS h 109 PHE 0.007 0.001 PHE b 61 TYR 0.035 0.002 TYR f 98 ARG 0.010 0.000 ARG b 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.112 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9312 (mp0) cc_final: 0.8980 (mp0) REVERT: a 60 LEU cc_start: 0.8782 (mt) cc_final: 0.8561 (mt) REVERT: a 81 ASP cc_start: 0.9061 (t0) cc_final: 0.8285 (p0) REVERT: a 90 MET cc_start: 0.9378 (mmp) cc_final: 0.9160 (mmm) REVERT: a 105 GLU cc_start: 0.9544 (mm-30) cc_final: 0.9197 (mm-30) REVERT: a 106 ASP cc_start: 0.8930 (m-30) cc_final: 0.8713 (m-30) REVERT: a 117 VAL cc_start: 0.9239 (m) cc_final: 0.8912 (p) REVERT: b 58 LEU cc_start: 0.9805 (tt) cc_final: 0.9514 (pp) REVERT: c 25 PHE cc_start: 0.8737 (m-80) cc_final: 0.8326 (m-80) REVERT: c 95 LYS cc_start: 0.9448 (ttmm) cc_final: 0.8968 (mppt) REVERT: d 99 ARG cc_start: 0.9234 (mtp85) cc_final: 0.8920 (mtp85) REVERT: e 90 MET cc_start: 0.8714 (tpt) cc_final: 0.8436 (tpt) REVERT: e 104 PHE cc_start: 0.9307 (m-10) cc_final: 0.8922 (m-80) REVERT: e 105 GLU cc_start: 0.9428 (pm20) cc_final: 0.9159 (pm20) REVERT: e 106 ASP cc_start: 0.9408 (m-30) cc_final: 0.8980 (m-30) REVERT: f 58 LEU cc_start: 0.9749 (tt) cc_final: 0.9465 (pp) REVERT: f 72 TYR cc_start: 0.9466 (m-80) cc_final: 0.9236 (m-80) REVERT: f 85 ASP cc_start: 0.8506 (m-30) cc_final: 0.8204 (m-30) REVERT: g 36 LYS cc_start: 0.9065 (mptt) cc_final: 0.8759 (mmtm) REVERT: g 61 GLU cc_start: 0.9440 (tm-30) cc_final: 0.9038 (tm-30) REVERT: h 71 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8540 (mm-30) outliers start: 2 outliers final: 2 residues processed: 153 average time/residue: 0.2701 time to fit residues: 59.2389 Evaluate side-chains 109 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14846 Z= 0.270 Angle : 0.625 7.372 21563 Z= 0.369 Chirality : 0.035 0.154 2456 Planarity : 0.004 0.041 1498 Dihedral : 32.377 174.888 4809 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.14 % Allowed : 1.15 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.28), residues: 825 helix: 1.62 (0.21), residues: 580 sheet: -1.71 (1.76), residues: 10 loop : -0.51 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS b 75 PHE 0.011 0.001 PHE f 100 TYR 0.017 0.002 TYR e 54 ARG 0.009 0.001 ARG b 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.005 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: symmetry clash REVERT: a 105 GLU cc_start: 0.9546 (mm-30) cc_final: 0.9245 (mm-30) REVERT: b 58 LEU cc_start: 0.9837 (tt) cc_final: 0.9528 (pp) REVERT: c 25 PHE cc_start: 0.8698 (m-80) cc_final: 0.8276 (m-80) REVERT: c 90 ASP cc_start: 0.8359 (t0) cc_final: 0.8139 (t0) REVERT: c 95 LYS cc_start: 0.9441 (ttmm) cc_final: 0.8975 (mppt) REVERT: d 85 LYS cc_start: 0.9573 (mppt) cc_final: 0.9365 (mmtm) REVERT: d 99 ARG cc_start: 0.9289 (mtp85) cc_final: 0.8873 (ttm110) REVERT: d 113 GLU cc_start: 0.9239 (mp0) cc_final: 0.8850 (mp0) REVERT: e 50 GLU cc_start: 0.9666 (mp0) cc_final: 0.9397 (mp0) REVERT: e 90 MET cc_start: 0.8882 (tpt) cc_final: 0.8626 (tpt) REVERT: e 104 PHE cc_start: 0.9506 (m-10) cc_final: 0.8942 (m-80) REVERT: e 106 ASP cc_start: 0.9502 (m-30) cc_final: 0.9108 (m-30) REVERT: e 120 MET cc_start: 0.6624 (mtt) cc_final: 0.6410 (mtt) REVERT: f 44 LYS cc_start: 0.9199 (tttt) cc_final: 0.8983 (tttt) REVERT: f 58 LEU cc_start: 0.9793 (tt) cc_final: 0.9417 (pp) REVERT: f 59 LYS cc_start: 0.9804 (ptmm) cc_final: 0.9502 (ptmm) REVERT: f 85 ASP cc_start: 0.8468 (m-30) cc_final: 0.8215 (m-30) REVERT: g 61 GLU cc_start: 0.9461 (tm-30) cc_final: 0.9027 (tm-30) REVERT: h 52 THR cc_start: 0.8239 (m) cc_final: 0.7828 (p) REVERT: h 71 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8527 (mm-30) outliers start: 1 outliers final: 1 residues processed: 132 average time/residue: 0.2645 time to fit residues: 50.5234 Evaluate side-chains 102 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14846 Z= 0.265 Angle : 0.639 8.835 21563 Z= 0.376 Chirality : 0.035 0.188 2456 Planarity : 0.004 0.044 1498 Dihedral : 32.430 175.796 4809 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.28), residues: 825 helix: 1.50 (0.21), residues: 580 sheet: -1.74 (1.78), residues: 10 loop : -0.54 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS b 75 PHE 0.014 0.001 PHE f 100 TYR 0.041 0.002 TYR b 88 ARG 0.007 0.001 ARG b 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.028 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: symmetry clash REVERT: a 105 GLU cc_start: 0.9552 (mm-30) cc_final: 0.9244 (mm-30) REVERT: b 58 LEU cc_start: 0.9831 (tt) cc_final: 0.9518 (pp) REVERT: b 84 MET cc_start: 0.9181 (tpp) cc_final: 0.8980 (tpp) REVERT: c 25 PHE cc_start: 0.8717 (m-80) cc_final: 0.8228 (m-80) REVERT: c 90 ASP cc_start: 0.8345 (t0) cc_final: 0.8101 (t0) REVERT: c 95 LYS cc_start: 0.9445 (ttmm) cc_final: 0.8988 (mppt) REVERT: d 85 LYS cc_start: 0.9604 (mppt) cc_final: 0.9402 (mmtm) REVERT: d 99 ARG cc_start: 0.9269 (mtp85) cc_final: 0.8819 (ttm110) REVERT: e 50 GLU cc_start: 0.9667 (mp0) cc_final: 0.9285 (mp0) REVERT: e 90 MET cc_start: 0.8862 (tpt) cc_final: 0.8609 (tpt) REVERT: e 104 PHE cc_start: 0.9260 (m-10) cc_final: 0.8937 (m-80) REVERT: e 106 ASP cc_start: 0.9085 (m-30) cc_final: 0.8646 (m-30) REVERT: f 44 LYS cc_start: 0.9168 (tttt) cc_final: 0.8968 (tttt) REVERT: f 58 LEU cc_start: 0.9819 (tt) cc_final: 0.9540 (pp) REVERT: f 85 ASP cc_start: 0.8376 (m-30) cc_final: 0.8165 (m-30) REVERT: g 61 GLU cc_start: 0.9461 (tm-30) cc_final: 0.9033 (tm-30) REVERT: h 52 THR cc_start: 0.8208 (m) cc_final: 0.7801 (p) REVERT: h 71 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8520 (mm-30) REVERT: h 102 LEU cc_start: 0.9432 (mp) cc_final: 0.8884 (tp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2674 time to fit residues: 53.2412 Evaluate side-chains 103 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 0.0770 chunk 79 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14846 Z= 0.284 Angle : 0.654 9.053 21563 Z= 0.384 Chirality : 0.036 0.177 2456 Planarity : 0.004 0.045 1498 Dihedral : 32.453 174.745 4809 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 825 helix: 1.43 (0.21), residues: 580 sheet: -1.86 (1.79), residues: 10 loop : -0.55 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS h 109 PHE 0.010 0.002 PHE d 65 TYR 0.046 0.002 TYR b 88 ARG 0.006 0.001 ARG b 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9325 (mp0) cc_final: 0.8982 (mp0) REVERT: a 105 GLU cc_start: 0.9536 (mm-30) cc_final: 0.9209 (mm-30) REVERT: a 120 MET cc_start: 0.8558 (mpp) cc_final: 0.8249 (mpp) REVERT: b 58 LEU cc_start: 0.9825 (tt) cc_final: 0.9527 (pp) REVERT: b 84 MET cc_start: 0.9198 (tpp) cc_final: 0.8996 (tpp) REVERT: c 25 PHE cc_start: 0.8732 (m-80) cc_final: 0.8248 (m-80) REVERT: c 90 ASP cc_start: 0.8335 (t0) cc_final: 0.7968 (t0) REVERT: c 95 LYS cc_start: 0.9449 (ttmm) cc_final: 0.8994 (mppt) REVERT: d 99 ARG cc_start: 0.9253 (mtp85) cc_final: 0.8799 (ttm110) REVERT: e 50 GLU cc_start: 0.9660 (mp0) cc_final: 0.9309 (mp0) REVERT: e 90 MET cc_start: 0.8774 (tpt) cc_final: 0.8491 (tpt) REVERT: e 104 PHE cc_start: 0.9370 (m-10) cc_final: 0.8809 (m-80) REVERT: e 105 GLU cc_start: 0.9462 (pm20) cc_final: 0.9157 (pm20) REVERT: e 106 ASP cc_start: 0.9177 (m-30) cc_final: 0.8860 (m-30) REVERT: e 124 ILE cc_start: 0.9609 (tt) cc_final: 0.9387 (tt) REVERT: f 44 LYS cc_start: 0.9156 (tttt) cc_final: 0.8943 (tttt) REVERT: f 58 LEU cc_start: 0.9807 (tt) cc_final: 0.9520 (pp) REVERT: f 59 LYS cc_start: 0.9804 (ptmm) cc_final: 0.9496 (ptmm) REVERT: f 72 TYR cc_start: 0.9546 (m-80) cc_final: 0.9288 (m-80) REVERT: f 85 ASP cc_start: 0.8475 (m-30) cc_final: 0.8171 (m-30) REVERT: g 61 GLU cc_start: 0.9458 (tm-30) cc_final: 0.9039 (tm-30) REVERT: h 52 THR cc_start: 0.8246 (m) cc_final: 0.7849 (p) REVERT: h 71 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8515 (mm-30) REVERT: h 102 LEU cc_start: 0.9478 (mp) cc_final: 0.8896 (tp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2740 time to fit residues: 54.2894 Evaluate side-chains 97 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 112 optimal weight: 40.0000 chunk 103 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 93 GLN ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14846 Z= 0.285 Angle : 0.656 9.094 21563 Z= 0.386 Chirality : 0.036 0.174 2456 Planarity : 0.004 0.043 1498 Dihedral : 32.476 174.756 4809 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 825 helix: 1.37 (0.21), residues: 580 sheet: -1.85 (1.80), residues: 10 loop : -0.58 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS h 109 PHE 0.016 0.002 PHE a 104 TYR 0.042 0.002 TYR b 88 ARG 0.007 0.001 ARG h 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9319 (mp0) cc_final: 0.8969 (mp0) REVERT: a 61 LEU cc_start: 0.8770 (tp) cc_final: 0.8429 (tp) REVERT: a 105 GLU cc_start: 0.9542 (mm-30) cc_final: 0.9267 (mm-30) REVERT: a 120 MET cc_start: 0.8574 (mpp) cc_final: 0.8268 (mpp) REVERT: b 58 LEU cc_start: 0.9834 (tt) cc_final: 0.9532 (pp) REVERT: c 25 PHE cc_start: 0.8728 (m-80) cc_final: 0.8227 (m-80) REVERT: c 95 LYS cc_start: 0.9453 (ttmm) cc_final: 0.9002 (mppt) REVERT: d 99 ARG cc_start: 0.9235 (mtp85) cc_final: 0.8775 (ttm110) REVERT: e 50 GLU cc_start: 0.9481 (mp0) cc_final: 0.9260 (mp0) REVERT: e 90 MET cc_start: 0.8773 (tpt) cc_final: 0.8532 (tpt) REVERT: e 104 PHE cc_start: 0.9399 (m-10) cc_final: 0.8855 (m-80) REVERT: e 105 GLU cc_start: 0.9454 (pm20) cc_final: 0.9155 (pm20) REVERT: e 106 ASP cc_start: 0.9112 (m-30) cc_final: 0.8806 (m-30) REVERT: e 125 GLN cc_start: 0.9482 (mp10) cc_final: 0.9187 (mp10) REVERT: f 58 LEU cc_start: 0.9813 (tt) cc_final: 0.9508 (pp) REVERT: f 59 LYS cc_start: 0.9797 (ptmm) cc_final: 0.9505 (ptmm) REVERT: f 72 TYR cc_start: 0.9547 (m-80) cc_final: 0.9317 (m-80) REVERT: f 85 ASP cc_start: 0.8557 (m-30) cc_final: 0.8248 (m-30) REVERT: g 61 GLU cc_start: 0.9469 (tm-30) cc_final: 0.9047 (tm-30) REVERT: h 71 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8511 (mm-30) REVERT: h 102 LEU cc_start: 0.9482 (mp) cc_final: 0.8922 (tp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2608 time to fit residues: 52.2937 Evaluate side-chains 103 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.029091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.021747 restraints weight = 165193.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.022564 restraints weight = 79062.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.023126 restraints weight = 48070.264| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14846 Z= 0.203 Angle : 0.628 7.488 21563 Z= 0.368 Chirality : 0.035 0.170 2456 Planarity : 0.004 0.047 1498 Dihedral : 32.288 175.154 4809 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.29), residues: 825 helix: 1.54 (0.21), residues: 580 sheet: -1.94 (1.73), residues: 10 loop : -0.56 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS h 109 PHE 0.008 0.001 PHE f 100 TYR 0.037 0.002 TYR b 88 ARG 0.006 0.000 ARG b 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2066.05 seconds wall clock time: 40 minutes 4.35 seconds (2404.35 seconds total)