Starting phenix.real_space_refine (version: dev) on Tue Feb 21 23:50:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfe_13373/02_2023/7pfe_13373.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfe_13373/02_2023/7pfe_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_13373/02_2023/7pfe_13373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfe_13373/02_2023/7pfe_13373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfe_13373/02_2023/7pfe_13373.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfe_13373/02_2023/7pfe_13373.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 8.04, per 1000 atoms: 0.58 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: 8.55 Conformation dependent library (CDL) restraints added in 1.1 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: 6.14 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: 7.38 Time building geometry restraints manager: 8.90 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: 5898 35.97 - 71.93: 1778 71.93 - 107.90: 25 107.90 - 143.86: 4 143.86 - 179.83: 2 Dihedral angle restraints: 7707 sinusoidal: 5276 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 7704 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 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. 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: 1.420 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: 7.300 Check model and map are aligned: 0.200 Process input model: 47.940 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 29.841 179.829 6141 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 % 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 *********************** 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 : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2919 time to fit residues: 66.0749 Evaluate side-chains 97 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2587 ------------------------------------------------------------------------------- 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: 0.8980 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: 4.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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: 0.8497 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 14846 Z= 0.327 Angle : 0.676 8.742 21563 Z= 0.402 Chirality : 0.037 0.145 2456 Planarity : 0.005 0.058 1498 Dihedral : 33.262 177.228 4489 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.27), residues: 825 helix: 1.05 (0.20), residues: 578 sheet: -2.16 (1.37), residues: 10 loop : -0.46 (0.35), residues: 237 *********************** 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 132 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.052 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 outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.2666 time to fit residues: 50.9903 Evaluate side-chains 90 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1882 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 102 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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** b 75 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 14846 Z= 0.218 Angle : 0.609 7.470 21563 Z= 0.364 Chirality : 0.034 0.159 2456 Planarity : 0.004 0.056 1498 Dihedral : 33.110 176.713 4489 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.28), residues: 825 helix: 1.46 (0.21), residues: 580 sheet: -1.78 (1.50), residues: 10 loop : -0.36 (0.36), residues: 235 *********************** 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 148 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.042 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 outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2789 time to fit residues: 58.9771 Evaluate side-chains 97 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2158 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** b 75 HIS ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 14846 Z= 0.383 Angle : 0.687 9.569 21563 Z= 0.405 Chirality : 0.037 0.162 2456 Planarity : 0.005 0.052 1498 Dihedral : 33.309 173.875 4489 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.28), residues: 825 helix: 1.27 (0.21), residues: 576 sheet: -1.55 (1.75), residues: 10 loop : -0.34 (0.36), residues: 239 *********************** 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 132 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.056 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 outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2717 time to fit residues: 52.0368 Evaluate side-chains 92 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3036 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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** c 94 ASN ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 14846 Z= 0.400 Angle : 0.704 10.208 21563 Z= 0.413 Chirality : 0.038 0.162 2456 Planarity : 0.005 0.040 1498 Dihedral : 33.561 177.603 4489 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.87 % 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: 0.85 (0.28), residues: 825 helix: 1.05 (0.21), residues: 578 sheet: -1.75 (1.81), residues: 10 loop : -0.35 (0.37), residues: 237 *********************** 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 130 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 1.349 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 outliers start: 6 outliers final: 4 residues processed: 128 average time/residue: 0.2926 time to fit residues: 53.7669 Evaluate side-chains 85 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2107 time to fit residues: 2.4206 ------------------------------------------------------------------------------- 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: 0.9980 chunk 26 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3701 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= 0.189 Angle : 0.612 6.895 21563 Z= 0.363 Chirality : 0.034 0.153 2456 Planarity : 0.004 0.040 1498 Dihedral : 33.224 179.477 4489 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.72 % 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: 1.25 (0.28), residues: 825 helix: 1.46 (0.21), residues: 580 sheet: -1.59 (1.76), residues: 10 loop : -0.57 (0.37), residues: 235 *********************** 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 155 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 151 average time/residue: 0.2858 time to fit residues: 61.7126 Evaluate side-chains 99 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1650 time to fit residues: 1.8547 ------------------------------------------------------------------------------- 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: 2.9990 chunk 62 optimal weight: 0.0270 chunk 79 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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** b 75 HIS ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14846 Z= 0.184 Angle : 0.606 7.639 21563 Z= 0.358 Chirality : 0.034 0.164 2456 Planarity : 0.004 0.047 1498 Dihedral : 32.886 176.703 4489 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.28), residues: 825 helix: 1.51 (0.21), residues: 582 sheet: -1.62 (1.72), residues: 10 loop : -0.64 (0.36), residues: 233 *********************** 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 150 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.068 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 outliers start: 1 outliers final: 1 residues processed: 149 average time/residue: 0.2676 time to fit residues: 58.0463 Evaluate side-chains 101 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1584 time to fit residues: 1.4924 ------------------------------------------------------------------------------- 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: 7.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 14846 Z= 0.311 Angle : 0.664 8.952 21563 Z= 0.391 Chirality : 0.036 0.200 2456 Planarity : 0.005 0.043 1498 Dihedral : 33.078 174.845 4489 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 825 helix: 1.33 (0.21), residues: 584 sheet: -1.66 (1.81), residues: 10 loop : -0.48 (0.38), residues: 231 *********************** 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 132 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2593 time to fit residues: 50.4258 Evaluate side-chains 92 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0582 ------------------------------------------------------------------------------- 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: 7.9990 chunk 104 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 30.0000 chunk 65 optimal weight: 6.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- 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** d 109 HIS ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 14846 Z= 0.353 Angle : 0.701 9.430 21563 Z= 0.410 Chirality : 0.037 0.187 2456 Planarity : 0.005 0.041 1498 Dihedral : 33.395 176.059 4489 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 24.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.28), residues: 825 helix: 1.05 (0.21), residues: 582 sheet: -1.76 (1.85), residues: 10 loop : -0.54 (0.38), residues: 233 *********************** 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 126 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2798 time to fit residues: 51.0334 Evaluate side-chains 90 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2564 ------------------------------------------------------------------------------- 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: 2.9990 chunk 74 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 0.0050 chunk 69 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 overall best weight: 3.3800 ------------------------------------------------------------------------------- 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** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 14846 Z= 0.303 Angle : 0.687 9.637 21563 Z= 0.402 Chirality : 0.037 0.234 2456 Planarity : 0.005 0.043 1498 Dihedral : 33.380 175.908 4489 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.28), residues: 825 helix: 0.93 (0.21), residues: 584 sheet: -1.80 (1.83), residues: 10 loop : -0.47 (0.39), residues: 231 ********************** 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 132 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2770 time to fit residues: 52.8482 Evaluate side-chains 92 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2727 ------------------------------------------------------------------------------- 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: 0.9980 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.029018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.021584 restraints weight = 168480.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.022363 restraints weight = 80950.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.022912 restraints weight = 50023.648| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 14846 Z= 0.212 Angle : 0.653 7.458 21563 Z= 0.384 Chirality : 0.035 0.194 2456 Planarity : 0.004 0.048 1498 Dihedral : 33.088 176.257 4489 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.28), residues: 825 helix: 1.11 (0.21), residues: 586 sheet: -1.76 (1.82), residues: 10 loop : -0.55 (0.39), residues: 229 =============================================================================== Job complete usr+sys time: 1955.93 seconds wall clock time: 36 minutes 49.54 seconds (2209.54 seconds total)