Starting phenix.real_space_refine on Sat Mar 16 19:53:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evg_28628/03_2024/8evg_28628.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evg_28628/03_2024/8evg_28628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evg_28628/03_2024/8evg_28628.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evg_28628/03_2024/8evg_28628.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evg_28628/03_2024/8evg_28628.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evg_28628/03_2024/8evg_28628.pdb" } resolution = 2.75 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= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 32 5.16 5 C 8886 2.51 5 N 2827 2.21 5 O 3538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 63": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "M GLU 23": "OE1" <-> "OE2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "M GLU 84": "OE1" <-> "OE2" Residue "M GLU 251": "OE1" <-> "OE2" Residue "N GLU 32": "OE1" <-> "OE2" Residue "N GLU 35": "OE1" <-> "OE2" Residue "N GLU 68": "OE1" <-> "OE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 263": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15577 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3015 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3012 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "M" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 8.56, per 1000 atoms: 0.55 Number of scatterers: 15577 At special positions: 0 Unit cell: (138.336, 125.664, 124.608, 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 32 16.00 P 294 15.00 O 3538 8.00 N 2827 7.00 C 8886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 44 " - pdb=" SG CYS M 118 " distance=2.03 Simple disulfide: pdb=" SG CYS M 181 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 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: 7.21 Conformation dependent library (CDL) restraints added in 1.8 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 23 sheets defined 46.1% alpha, 18.2% beta 116 base pairs and 280 stacking pairs defined. Time for finding SS restraints: 7.60 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.525A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.776A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.590A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.639A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) 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: 3.746A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 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 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.587A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 52 No H-bonds generated for 'chain 'M' and resid 50 through 52' Processing helix chain 'M' and resid 237 through 241 removed outlier: 3.848A pdb=" N THR M 241 " --> pdb=" O SER M 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.845A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.597A 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: 6.577A 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 42 through 43 removed outlier: 7.177A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 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: 7.317A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 'M' and resid 25 through 26 Processing sheet with id=AB2, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.695A pdb=" N THR M 139 " --> pdb=" O GLU M 32 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N TYR M 54 " --> pdb=" O TYR M 74 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR M 74 " --> pdb=" O TYR M 54 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE M 56 " --> pdb=" O TYR M 72 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR M 72 " --> pdb=" O ILE M 56 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP M 58 " --> pdb=" O ILE M 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.695A pdb=" N THR M 139 " --> pdb=" O GLU M 32 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 40 through 43 Processing sheet with id=AB5, first strand: chain 'M' and resid 168 through 171 Processing sheet with id=AB6, first strand: chain 'M' and resid 177 through 180 removed outlier: 3.683A pdb=" N ASP M 228 " --> pdb=" O SER M 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 211 through 212 removed outlier: 6.531A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR M 255 " --> pdb=" O GLN M 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 26 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 3.676A pdb=" N GLY N 71 " --> pdb=" O TRP N 58 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU N 67 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 32 through 34 removed outlier: 4.191A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 40 through 43 Processing sheet with id=AC3, first strand: chain 'N' and resid 163 through 164 removed outlier: 3.624A pdb=" N VAL N 177 " --> pdb=" O ILE N 233 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.531A pdb=" N MET N 169 " --> pdb=" O GLU N 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'N' and resid 211 through 212 removed outlier: 6.439A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR N 255 " --> pdb=" O GLN N 248 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 277 hydrogen bonds 546 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 280 stacking parallelities Total time for adding SS restraints: 6.40 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1968 1.31 - 1.43: 6054 1.43 - 1.56: 7989 1.56 - 1.69: 408 1.69 - 1.82: 55 Bond restraints: 16474 Sorted by residual: bond pdb=" O3' DG I 117 " pdb=" P DG I 118 " ideal model delta sigma weight residual 1.607 1.339 0.268 1.50e-02 4.44e+03 3.19e+02 bond pdb=" O3' DG J 80 " pdb=" P DG J 81 " ideal model delta sigma weight residual 1.607 1.359 0.248 1.50e-02 4.44e+03 2.73e+02 bond pdb=" O3' DG I 85 " pdb=" P DA I 86 " ideal model delta sigma weight residual 1.607 1.364 0.243 1.50e-02 4.44e+03 2.62e+02 bond pdb=" O3' DC I 107 " pdb=" P DA I 108 " ideal model delta sigma weight residual 1.607 1.370 0.237 1.50e-02 4.44e+03 2.49e+02 bond pdb=" O3' DT I 35 " pdb=" P DG I 36 " ideal model delta sigma weight residual 1.607 1.376 0.231 1.50e-02 4.44e+03 2.38e+02 ... (remaining 16469 not shown) Histogram of bond angle deviations from ideal: 79.64 - 91.72: 13 91.72 - 103.80: 1308 103.80 - 115.87: 10948 115.87 - 127.95: 10717 127.95 - 140.03: 535 Bond angle restraints: 23521 Sorted by residual: angle pdb=" O3' DC I 96 " pdb=" C3' DC I 96 " pdb=" C2' DC I 96 " ideal model delta sigma weight residual 111.50 90.34 21.16 1.50e+00 4.44e-01 1.99e+02 angle pdb=" O3' DA J 82 " pdb=" C3' DA J 82 " pdb=" C2' DA J 82 " ideal model delta sigma weight residual 111.50 90.71 20.79 1.50e+00 4.44e-01 1.92e+02 angle pdb=" O3' DA J 97 " pdb=" C3' DA J 97 " pdb=" C2' DA J 97 " ideal model delta sigma weight residual 111.50 130.96 -19.46 1.50e+00 4.44e-01 1.68e+02 angle pdb=" C4' DT I 131 " pdb=" C3' DT I 131 " pdb=" O3' DT I 131 " ideal model delta sigma weight residual 110.00 129.08 -19.08 1.50e+00 4.44e-01 1.62e+02 angle pdb=" O3' DC J 19 " pdb=" C3' DC J 19 " pdb=" C2' DC J 19 " ideal model delta sigma weight residual 111.50 130.56 -19.06 1.50e+00 4.44e-01 1.62e+02 ... (remaining 23516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.94: 7209 32.94 - 65.88: 1834 65.88 - 98.82: 116 98.82 - 131.76: 2 131.76 - 164.70: 4 Dihedral angle restraints: 9165 sinusoidal: 5645 harmonic: 3520 Sorted by residual: dihedral pdb=" C4' DC I 20 " pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " pdb=" P DT I 21 " ideal model delta sinusoidal sigma weight residual -140.00 24.70 -164.70 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DT I 131 " pdb=" C3' DT I 131 " pdb=" O3' DT I 131 " pdb=" P DT I 132 " ideal model delta sinusoidal sigma weight residual -140.00 24.49 -164.49 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC I 92 " pdb=" C3' DC I 92 " pdb=" O3' DC I 92 " pdb=" P DT I 93 " ideal model delta sinusoidal sigma weight residual 220.00 62.35 157.65 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 9162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 2394 0.209 - 0.418: 211 0.418 - 0.627: 34 0.627 - 0.836: 11 0.836 - 1.045: 2 Chirality restraints: 2652 Sorted by residual: chirality pdb=" C3' DG I 53 " pdb=" C4' DG I 53 " pdb=" O3' DG I 53 " pdb=" C2' DG I 53 " both_signs ideal model delta sigma weight residual False -2.66 -1.61 -1.05 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" C3' DC I 92 " pdb=" C4' DC I 92 " pdb=" O3' DC I 92 " pdb=" C2' DC I 92 " both_signs ideal model delta sigma weight residual False -2.66 -1.68 -0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" P DT I 87 " pdb=" OP1 DT I 87 " pdb=" OP2 DT I 87 " pdb=" O5' DT I 87 " both_signs ideal model delta sigma weight residual True 2.35 -1.55 0.80 2.00e-01 2.50e+01 1.59e+01 ... (remaining 2649 not shown) Planarity restraints: 1948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 68 " -0.119 2.00e-02 2.50e+03 6.09e-02 9.28e+01 pdb=" N1 DT J 68 " 0.098 2.00e-02 2.50e+03 pdb=" C2 DT J 68 " 0.007 2.00e-02 2.50e+03 pdb=" O2 DT J 68 " 0.064 2.00e-02 2.50e+03 pdb=" N3 DT J 68 " -0.079 2.00e-02 2.50e+03 pdb=" C4 DT J 68 " -0.015 2.00e-02 2.50e+03 pdb=" O4 DT J 68 " -0.019 2.00e-02 2.50e+03 pdb=" C5 DT J 68 " 0.045 2.00e-02 2.50e+03 pdb=" C7 DT J 68 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT J 68 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 98 " 0.117 2.00e-02 2.50e+03 5.78e-02 9.19e+01 pdb=" N9 DA I 98 " -0.123 2.00e-02 2.50e+03 pdb=" C8 DA I 98 " 0.029 2.00e-02 2.50e+03 pdb=" N7 DA I 98 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 98 " -0.023 2.00e-02 2.50e+03 pdb=" C6 DA I 98 " -0.012 2.00e-02 2.50e+03 pdb=" N6 DA I 98 " 0.024 2.00e-02 2.50e+03 pdb=" N1 DA I 98 " 0.061 2.00e-02 2.50e+03 pdb=" C2 DA I 98 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DA I 98 " -0.040 2.00e-02 2.50e+03 pdb=" C4 DA I 98 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 122 " 0.098 2.00e-02 2.50e+03 5.04e-02 7.61e+01 pdb=" N9 DG J 122 " -0.063 2.00e-02 2.50e+03 pdb=" C8 DG J 122 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG J 122 " -0.019 2.00e-02 2.50e+03 pdb=" C5 DG J 122 " 0.034 2.00e-02 2.50e+03 pdb=" C6 DG J 122 " 0.029 2.00e-02 2.50e+03 pdb=" O6 DG J 122 " -0.019 2.00e-02 2.50e+03 pdb=" N1 DG J 122 " 0.050 2.00e-02 2.50e+03 pdb=" C2 DG J 122 " 0.012 2.00e-02 2.50e+03 pdb=" N2 DG J 122 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DG J 122 " -0.104 2.00e-02 2.50e+03 pdb=" C4 DG J 122 " -0.026 2.00e-02 2.50e+03 ... (remaining 1945 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 27 2.42 - 3.04: 8939 3.04 - 3.66: 23614 3.66 - 4.28: 41684 4.28 - 4.90: 62662 Nonbonded interactions: 136926 Sorted by model distance: nonbonded pdb=" N2 DG I 109 " pdb=" O2 DC J 54 " model vdw 1.794 2.520 nonbonded pdb=" N2 DG I 25 " pdb=" O2 DC J 138 " model vdw 1.815 2.496 nonbonded pdb=" O2 DC I 134 " pdb=" N2 DG J 29 " model vdw 2.066 2.496 nonbonded pdb=" OD2 ASP M 95 " pdb=" OG SER M 98 " model vdw 2.219 2.440 nonbonded pdb=" N2 DG I 53 " pdb=" O2 DT J 111 " model vdw 2.227 2.520 ... (remaining 136921 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' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.720 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 49.210 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 0.020 0.268 16474 Z= 0.985 Angle : 2.030 29.362 23521 Z= 1.164 Chirality : 0.131 1.045 2652 Planarity : 0.010 0.086 1948 Dihedral : 28.950 164.699 6897 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.29 % Allowed : 20.41 % Favored : 79.30 % 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: 1.12 (0.25), residues: 1188 helix: 2.19 (0.22), residues: 543 sheet: -0.04 (0.35), residues: 226 loop : -0.74 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 69 HIS 0.004 0.001 HIS M 249 PHE 0.013 0.001 PHE D 67 TYR 0.024 0.001 TYR H 37 ARG 0.008 0.000 ARG N 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 288 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.7907 (mtt) cc_final: 0.7703 (mtt) outliers start: 3 outliers final: 1 residues processed: 289 average time/residue: 1.7463 time to fit residues: 540.3997 Evaluate side-chains 191 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 25 ASN D 46 HIS E 39 HIS E 108 ASN E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 81 ASN N 25 GLN N 196 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16474 Z= 0.266 Angle : 0.680 9.089 23521 Z= 0.392 Chirality : 0.041 0.266 2652 Planarity : 0.005 0.049 1948 Dihedral : 30.501 176.716 4574 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.40 % Allowed : 23.13 % Favored : 73.47 % 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: 1.45 (0.25), residues: 1188 helix: 2.52 (0.22), residues: 545 sheet: 0.21 (0.35), residues: 226 loop : -0.73 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 132 HIS 0.007 0.001 HIS A 39 PHE 0.008 0.001 PHE A 67 TYR 0.011 0.001 TYR N 117 ARG 0.006 0.001 ARG N 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 209 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 TYR cc_start: 0.7799 (t80) cc_final: 0.7482 (t80) outliers start: 35 outliers final: 6 residues processed: 231 average time/residue: 1.6400 time to fit residues: 408.5607 Evaluate side-chains 188 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 182 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 223 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 108 ASN D 46 HIS D 64 ASN E 39 HIS E 55 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16474 Z= 0.262 Angle : 0.619 8.945 23521 Z= 0.358 Chirality : 0.038 0.175 2652 Planarity : 0.004 0.038 1948 Dihedral : 30.275 179.141 4573 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.82 % Allowed : 24.30 % Favored : 72.89 % 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: 1.45 (0.25), residues: 1188 helix: 2.60 (0.22), residues: 543 sheet: 0.27 (0.35), residues: 226 loop : -0.88 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 199 HIS 0.006 0.001 HIS A 39 PHE 0.009 0.001 PHE A 67 TYR 0.014 0.001 TYR H 37 ARG 0.007 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 213 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 56 MET cc_start: 0.8096 (tpp) cc_final: 0.7722 (tpt) outliers start: 29 outliers final: 13 residues processed: 228 average time/residue: 1.6764 time to fit residues: 411.5494 Evaluate side-chains 204 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 172 SER Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain M residue 239 ASP Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 139 optimal weight: 0.0020 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 overall best weight: 1.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN N 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16474 Z= 0.238 Angle : 0.590 8.665 23521 Z= 0.343 Chirality : 0.037 0.144 2652 Planarity : 0.004 0.063 1948 Dihedral : 29.976 179.721 4573 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.82 % Allowed : 24.39 % Favored : 72.79 % 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: 1.52 (0.25), residues: 1188 helix: 2.70 (0.22), residues: 542 sheet: 0.30 (0.35), residues: 226 loop : -0.89 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 132 HIS 0.005 0.001 HIS A 39 PHE 0.009 0.001 PHE A 67 TYR 0.014 0.001 TYR H 37 ARG 0.007 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 TYR cc_start: 0.7809 (t80) cc_final: 0.7385 (t80) outliers start: 29 outliers final: 15 residues processed: 214 average time/residue: 1.5342 time to fit residues: 355.3267 Evaluate side-chains 194 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain M residue 239 ASP Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 214 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16474 Z= 0.342 Angle : 0.621 8.659 23521 Z= 0.357 Chirality : 0.039 0.155 2652 Planarity : 0.004 0.043 1948 Dihedral : 30.203 179.416 4573 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.53 % Allowed : 24.68 % Favored : 72.79 % 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 (0.25), residues: 1188 helix: 2.51 (0.22), residues: 542 sheet: 0.17 (0.35), residues: 226 loop : -0.98 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 58 HIS 0.005 0.001 HIS M 249 PHE 0.010 0.001 PHE E 67 TYR 0.014 0.002 TYR H 37 ARG 0.011 0.001 ARG M 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 39 TYR cc_start: 0.7922 (t80) cc_final: 0.7467 (t80) REVERT: G 56 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7635 (tt0) outliers start: 26 outliers final: 14 residues processed: 202 average time/residue: 1.6750 time to fit residues: 365.0273 Evaluate side-chains 190 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 175 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 212 LEU Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 0.0670 chunk 139 optimal weight: 0.2980 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16474 Z= 0.179 Angle : 0.570 8.437 23521 Z= 0.331 Chirality : 0.035 0.138 2652 Planarity : 0.004 0.038 1948 Dihedral : 29.736 179.114 4573 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.75 % Allowed : 26.04 % Favored : 72.21 % 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: 1.58 (0.25), residues: 1188 helix: 2.79 (0.22), residues: 541 sheet: 0.17 (0.35), residues: 226 loop : -0.81 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 58 HIS 0.004 0.001 HIS A 39 PHE 0.010 0.001 PHE A 67 TYR 0.012 0.001 TYR H 37 ARG 0.008 0.000 ARG M 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 56 MET cc_start: 0.7993 (tpp) cc_final: 0.7711 (tpt) outliers start: 18 outliers final: 10 residues processed: 202 average time/residue: 1.6167 time to fit residues: 351.9437 Evaluate side-chains 190 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 180 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 219 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 138 optimal weight: 0.0170 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN M 61 GLN M 196 GLN N 57 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16474 Z= 0.248 Angle : 0.588 8.767 23521 Z= 0.337 Chirality : 0.036 0.142 2652 Planarity : 0.004 0.045 1948 Dihedral : 29.808 178.969 4573 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.43 % Allowed : 26.34 % Favored : 71.23 % 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: 1.51 (0.25), residues: 1188 helix: 2.71 (0.22), residues: 541 sheet: 0.12 (0.35), residues: 226 loop : -0.82 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 132 HIS 0.005 0.001 HIS E 39 PHE 0.008 0.001 PHE A 67 TYR 0.014 0.001 TYR H 37 ARG 0.012 0.000 ARG M 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 1.311 Fit side-chains revert: symmetry clash REVERT: D 39 TYR cc_start: 0.7793 (t80) cc_final: 0.7338 (t80) REVERT: E 39 HIS cc_start: 0.7112 (t70) cc_final: 0.6861 (t70) REVERT: E 97 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: G 56 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: H 56 MET cc_start: 0.8032 (tpp) cc_final: 0.7709 (tpt) outliers start: 25 outliers final: 15 residues processed: 196 average time/residue: 1.6669 time to fit residues: 352.1417 Evaluate side-chains 189 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 219 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.0040 chunk 88 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16474 Z= 0.226 Angle : 0.590 11.559 23521 Z= 0.336 Chirality : 0.036 0.138 2652 Planarity : 0.004 0.050 1948 Dihedral : 29.670 178.932 4573 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.53 % Allowed : 26.63 % Favored : 70.85 % 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: 1.52 (0.25), residues: 1188 helix: 2.70 (0.22), residues: 541 sheet: 0.14 (0.35), residues: 226 loop : -0.78 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 132 HIS 0.004 0.001 HIS E 39 PHE 0.009 0.001 PHE A 67 TYR 0.014 0.001 TYR H 37 ARG 0.014 0.000 ARG M 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: D 39 TYR cc_start: 0.7782 (t80) cc_final: 0.7327 (t80) REVERT: D 46 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.6508 (m90) REVERT: E 39 HIS cc_start: 0.7131 (t70) cc_final: 0.6892 (t70) REVERT: E 97 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: G 56 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: H 56 MET cc_start: 0.8009 (tpp) cc_final: 0.7713 (tpt) outliers start: 26 outliers final: 16 residues processed: 194 average time/residue: 1.7301 time to fit residues: 363.0530 Evaluate side-chains 190 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 212 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 219 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS G 73 ASN N 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 16474 Z= 0.439 Angle : 0.665 11.587 23521 Z= 0.374 Chirality : 0.041 0.148 2652 Planarity : 0.005 0.047 1948 Dihedral : 30.146 178.772 4573 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.53 % Allowed : 26.82 % Favored : 70.65 % 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: 1.15 (0.25), residues: 1188 helix: 2.38 (0.22), residues: 542 sheet: -0.04 (0.34), residues: 220 loop : -0.94 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 132 HIS 0.005 0.001 HIS N 249 PHE 0.011 0.002 PHE F 61 TYR 0.014 0.002 TYR H 37 ARG 0.013 0.001 ARG M 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: D 39 TYR cc_start: 0.7968 (t80) cc_final: 0.7493 (t80) REVERT: E 97 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: G 56 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: H 56 MET cc_start: 0.8081 (tpp) cc_final: 0.7687 (tpt) outliers start: 26 outliers final: 18 residues processed: 199 average time/residue: 1.7006 time to fit residues: 364.2056 Evaluate side-chains 198 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 178 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 212 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 219 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16474 Z= 0.245 Angle : 0.611 10.750 23521 Z= 0.347 Chirality : 0.036 0.159 2652 Planarity : 0.004 0.042 1948 Dihedral : 29.780 178.421 4573 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.65 % Allowed : 27.41 % Favored : 70.94 % 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: 1.36 (0.25), residues: 1188 helix: 2.53 (0.22), residues: 542 sheet: 0.07 (0.35), residues: 218 loop : -0.81 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 132 HIS 0.004 0.001 HIS A 39 PHE 0.009 0.001 PHE A 67 TYR 0.015 0.001 TYR H 37 ARG 0.012 0.001 ARG M 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: D 39 TYR cc_start: 0.7881 (t80) cc_final: 0.7452 (t80) REVERT: E 97 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: G 56 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: H 56 MET cc_start: 0.7999 (tpp) cc_final: 0.7625 (tpt) REVERT: N 32 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6811 (mp0) outliers start: 17 outliers final: 12 residues processed: 191 average time/residue: 1.7295 time to fit residues: 355.6753 Evaluate side-chains 191 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 177 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 42 MET Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS N 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.104797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.067652 restraints weight = 30571.510| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.03 r_work: 0.2867 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16474 Z= 0.213 Angle : 0.602 10.119 23521 Z= 0.341 Chirality : 0.036 0.148 2652 Planarity : 0.004 0.058 1948 Dihedral : 29.672 178.778 4573 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.94 % Allowed : 27.50 % Favored : 70.55 % 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 (0.25), residues: 1188 helix: 2.60 (0.22), residues: 542 sheet: 0.13 (0.35), residues: 218 loop : -0.69 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 132 HIS 0.004 0.001 HIS M 249 PHE 0.009 0.001 PHE A 67 TYR 0.016 0.001 TYR E 54 ARG 0.017 0.001 ARG F 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6174.42 seconds wall clock time: 109 minutes 30.71 seconds (6570.71 seconds total)