Starting phenix.real_space_refine on Fri Feb 16 14:23:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0j_26261/02_2024/7u0j_26261.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0j_26261/02_2024/7u0j_26261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0j_26261/02_2024/7u0j_26261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0j_26261/02_2024/7u0j_26261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0j_26261/02_2024/7u0j_26261.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0j_26261/02_2024/7u0j_26261.pdb" } resolution = 2.7 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= 0.005 sd= 0.103 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 298 5.49 5 S 32 5.16 5 C 8914 2.51 5 N 2817 2.21 5 O 3561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "K GLU 175": "OE1" <-> "OE2" Residue "N GLU 68": "OE1" <-> "OE2" Residue "N GLU 84": "OE1" <-> "OE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N GLU 175": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15622 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" 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: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} 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: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3084 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3025 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "K" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1759 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 8.40, per 1000 atoms: 0.54 Number of scatterers: 15622 At special positions: 0 Unit cell: (139.392, 125.664, 128.832, 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 298 15.00 O 3561 8.00 N 2817 7.00 C 8914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS K 44 " - pdb=" SG CYS K 118 " distance=2.03 Simple disulfide: pdb=" SG CYS K 181 " - pdb=" SG CYS K 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: 7.01 Conformation dependent library (CDL) restraints added in 1.8 seconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 21 sheets defined 46.9% alpha, 19.8% beta 134 base pairs and 273 stacking pairs defined. Time for finding SS restraints: 6.66 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.592A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.804A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.726A 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 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.645A pdb=" N LEU C 55 " --> pdb=" O MET C 51 " (cutoff:3.500A) 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 removed outlier: 3.547A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.609A pdb=" N TYR D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.530A 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 131 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: 3.560A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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 removed outlier: 3.511A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.621A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.548A pdb=" N ASN H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 109 through 113 removed outlier: 4.114A pdb=" N SER K 113 " --> pdb=" O SER K 110 " (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 84 through 87 removed outlier: 3.828A pdb=" N LYS N 87 " --> pdb=" O GLU N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 87' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.674A pdb=" N ASP N 112 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 109 through 113' Processing helix chain 'N' and resid 237 through 241 removed outlier: 3.708A pdb=" N ASP N 240 " --> pdb=" O GLU N 237 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR N 241 " --> pdb=" O SER N 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 237 through 241' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.970A 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: 6.572A 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: 7.154A pdb=" N ARG C 42 " --> pdb=" O ILE D 90 " (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 83 through 84 removed outlier: 6.501A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.140A pdb=" N ARG G 42 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 25 through 28 removed outlier: 3.564A pdb=" N VAL K 101 " --> pdb=" O CYS K 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 32 through 34 removed outlier: 7.998A pdb=" N TYR K 54 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR K 74 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE K 56 " --> pdb=" O TYR K 72 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR K 72 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP K 58 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.501A pdb=" N MET K 169 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU K 191 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR K 207 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP K 193 " --> pdb=" O LEU K 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.501A pdb=" N MET K 169 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR K 255 " --> pdb=" O GLN K 248 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 177 through 180 Processing sheet with id=AB7, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AB8, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.274A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU N 67 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 4.029A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 39 through 43 Processing sheet with id=AC2, first strand: chain 'N' and resid 162 through 164 removed outlier: 3.956A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.816A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 324 hydrogen bonds 648 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 273 stacking parallelities Total time for adding SS restraints: 6.06 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 15 1.20 - 1.36: 4542 1.36 - 1.51: 7106 1.51 - 1.67: 4815 1.67 - 1.83: 51 Bond restraints: 16529 Sorted by residual: bond pdb=" C LEU B 90 " pdb=" O LEU B 90 " ideal model delta sigma weight residual 1.237 1.052 0.184 1.19e-02 7.06e+03 2.40e+02 bond pdb=" C MET C 51 " pdb=" O MET C 51 " ideal model delta sigma weight residual 1.236 1.045 0.192 1.29e-02 6.01e+03 2.20e+02 bond pdb=" C LEU C 93 " pdb=" O LEU C 93 " ideal model delta sigma weight residual 1.237 1.069 0.168 1.17e-02 7.31e+03 2.05e+02 bond pdb=" C ASN C 94 " pdb=" O ASN C 94 " ideal model delta sigma weight residual 1.237 1.087 0.150 1.17e-02 7.31e+03 1.65e+02 bond pdb=" CA MET C 51 " pdb=" C MET C 51 " ideal model delta sigma weight residual 1.523 1.361 0.161 1.37e-02 5.33e+03 1.39e+02 ... (remaining 16524 not shown) Histogram of bond angle deviations from ideal: 82.96 - 93.19: 2 93.19 - 103.42: 778 103.42 - 113.65: 10195 113.65 - 123.88: 11239 123.88 - 134.12: 1404 Bond angle restraints: 23618 Sorted by residual: angle pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" C SER H 33 " ideal model delta sigma weight residual 110.61 126.95 -16.34 1.25e+00 6.40e-01 1.71e+02 angle pdb=" CB MET C 51 " pdb=" CG MET C 51 " pdb=" SD MET C 51 " ideal model delta sigma weight residual 112.70 82.96 29.74 3.00e+00 1.11e-01 9.83e+01 angle pdb=" N LYS C 13 " pdb=" CA LYS C 13 " pdb=" C LYS C 13 " ideal model delta sigma weight residual 110.80 128.74 -17.94 2.13e+00 2.20e-01 7.10e+01 angle pdb=" C LYS C 13 " pdb=" N ALA C 14 " pdb=" CA ALA C 14 " ideal model delta sigma weight residual 121.54 134.09 -12.55 1.91e+00 2.74e-01 4.32e+01 angle pdb=" CA GLN B 93 " pdb=" CB GLN B 93 " pdb=" CG GLN B 93 " ideal model delta sigma weight residual 114.10 101.78 12.32 2.00e+00 2.50e-01 3.79e+01 ... (remaining 23613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.74: 7400 32.74 - 65.48: 1800 65.48 - 98.22: 38 98.22 - 130.95: 1 130.95 - 163.69: 3 Dihedral angle restraints: 9242 sinusoidal: 5730 harmonic: 3512 Sorted by residual: dihedral pdb=" C LEU E 82 " pdb=" N LEU E 82 " pdb=" CA LEU E 82 " pdb=" CB LEU E 82 " ideal model delta harmonic sigma weight residual -122.60 -108.48 -14.12 0 2.50e+00 1.60e-01 3.19e+01 dihedral pdb=" C SER H 33 " pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" CB SER H 33 " ideal model delta harmonic sigma weight residual -122.60 -134.48 11.88 0 2.50e+00 1.60e-01 2.26e+01 dihedral pdb=" CA PRO D 104 " pdb=" C PRO D 104 " pdb=" N GLY D 105 " pdb=" CA GLY D 105 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 9239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2621 0.137 - 0.275: 32 0.275 - 0.412: 6 0.412 - 0.549: 2 0.549 - 0.687: 2 Chirality restraints: 2663 Sorted by residual: chirality pdb=" CA SER H 33 " pdb=" N SER H 33 " pdb=" C SER H 33 " pdb=" CB SER H 33 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CG LEU C 93 " pdb=" CB LEU C 93 " pdb=" CD1 LEU C 93 " pdb=" CD2 LEU C 93 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA LYS C 13 " pdb=" N LYS C 13 " pdb=" C LYS C 13 " pdb=" CB LYS C 13 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.73e+00 ... (remaining 2660 not shown) Planarity restraints: 1949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 92 " 0.035 2.00e-02 2.50e+03 7.33e-02 5.37e+01 pdb=" C GLU C 92 " -0.127 2.00e-02 2.50e+03 pdb=" O GLU C 92 " 0.049 2.00e-02 2.50e+03 pdb=" N LEU C 93 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 51 " 0.027 2.00e-02 2.50e+03 5.37e-02 2.89e+01 pdb=" C MET C 51 " -0.093 2.00e-02 2.50e+03 pdb=" O MET C 51 " 0.035 2.00e-02 2.50e+03 pdb=" N ALA C 52 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 62 " 0.084 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO N 63 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO N 63 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO N 63 " 0.066 5.00e-02 4.00e+02 ... (remaining 1946 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 262 2.65 - 3.21: 11930 3.21 - 3.78: 28256 3.78 - 4.34: 38800 4.34 - 4.90: 56217 Nonbonded interactions: 135465 Sorted by model distance: nonbonded pdb=" O SER H 33 " pdb=" OG SER H 33 " model vdw 2.088 2.440 nonbonded pdb=" CG LYS C 13 " pdb=" N ALA C 14 " model vdw 2.181 3.520 nonbonded pdb=" CA MET C 51 " pdb=" SD MET C 51 " model vdw 2.308 3.064 nonbonded pdb=" O MET C 51 " pdb=" CG MET C 51 " model vdw 2.318 3.440 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.325 2.440 ... (remaining 135460 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' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 32 through 125) selection = (chain 'H' and resid 32 through 125) } ncs_group { reference = chain 'K' selection = (chain 'N' and (resid 23 through 187 or (resid 188 and (name N or name CA or nam \ e C or name O or name CB )) or resid 189 through 264 or (resid 265 and (name N o \ r name CA or name C or name O or name CB )))) } 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: 0.570 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: 3.890 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 47.260 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 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:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.192 16529 Z= 0.509 Angle : 0.933 29.745 23618 Z= 0.528 Chirality : 0.053 0.687 2663 Planarity : 0.007 0.126 1949 Dihedral : 27.006 163.693 6980 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 0.39 % Allowed : 21.92 % Favored : 77.69 % Cbeta Deviations : 0.27 % 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: -0.97 (0.22), residues: 1186 helix: -0.21 (0.19), residues: 537 sheet: -0.23 (0.34), residues: 234 loop : -1.27 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 58 HIS 0.006 0.002 HIS C 31 PHE 0.029 0.003 PHE A 78 TYR 0.045 0.002 TYR H 41 ARG 0.013 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: H 69 ASP cc_start: 0.8354 (t70) cc_final: 0.8114 (t0) outliers start: 4 outliers final: 1 residues processed: 176 average time/residue: 1.5952 time to fit residues: 303.3755 Evaluate side-chains 135 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 59 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 60 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** G 31 HIS ** 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: 0.7933 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16529 Z= 0.213 Angle : 0.565 7.608 23618 Z= 0.332 Chirality : 0.035 0.188 2663 Planarity : 0.005 0.080 1949 Dihedral : 29.560 151.995 4680 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.42 % Allowed : 22.41 % Favored : 74.17 % 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: 0.47 (0.24), residues: 1186 helix: 1.47 (0.22), residues: 548 sheet: -0.07 (0.34), residues: 234 loop : -1.02 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 58 HIS 0.005 0.001 HIS H 50 PHE 0.010 0.001 PHE N 229 TYR 0.026 0.001 TYR H 41 ARG 0.004 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 145 time to evaluate : 1.375 Fit side-chains REVERT: A 59 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.6888 (pp20) REVERT: A 106 ASP cc_start: 0.8001 (m-30) cc_final: 0.7798 (m-30) REVERT: D 77 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.6966 (tm-30) REVERT: E 50 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7610 (mt-10) REVERT: G 116 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8407 (mm) REVERT: H 69 ASP cc_start: 0.8376 (t70) cc_final: 0.8114 (t0) REVERT: K 57 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.7696 (mm110) REVERT: K 111 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8010 (pp20) outliers start: 35 outliers final: 15 residues processed: 163 average time/residue: 1.6916 time to fit residues: 299.0002 Evaluate side-chains 146 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 57 GLN Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 239 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 16529 Z= 0.465 Angle : 0.670 8.337 23618 Z= 0.385 Chirality : 0.042 0.147 2663 Planarity : 0.005 0.067 1949 Dihedral : 30.058 156.759 4680 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.89 % Allowed : 23.29 % Favored : 71.82 % 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: 0.49 (0.24), residues: 1186 helix: 1.55 (0.22), residues: 546 sheet: -0.15 (0.34), residues: 236 loop : -1.02 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 58 HIS 0.008 0.002 HIS C 31 PHE 0.013 0.002 PHE N 229 TYR 0.027 0.002 TYR H 41 ARG 0.006 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 135 time to evaluate : 1.313 Fit side-chains REVERT: A 59 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7059 (pp20) REVERT: B 79 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8046 (mttp) REVERT: C 24 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7454 (mp10) REVERT: C 51 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7337 (ttp) REVERT: C 91 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: D 77 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: E 120 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.7903 (mtt) REVERT: G 91 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: H 69 ASP cc_start: 0.8604 (t70) cc_final: 0.8305 (t0) REVERT: H 87 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7139 (mtt90) REVERT: K 57 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.7977 (mm110) REVERT: K 65 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8294 (mm-40) REVERT: K 103 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.6006 (tpt) REVERT: K 111 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8046 (pp20) REVERT: K 161 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7869 (ptpp) REVERT: K 235 ASN cc_start: 0.7517 (p0) cc_final: 0.7297 (p0) outliers start: 50 outliers final: 24 residues processed: 163 average time/residue: 1.5342 time to fit residues: 271.5440 Evaluate side-chains 165 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 128 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 57 GLN Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 239 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** 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: 0.7971 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16529 Z= 0.178 Angle : 0.590 10.202 23618 Z= 0.346 Chirality : 0.037 0.210 2663 Planarity : 0.004 0.055 1949 Dihedral : 30.022 156.195 4680 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.50 % Allowed : 23.48 % Favored : 72.02 % 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: 0.94 (0.25), residues: 1186 helix: 1.99 (0.22), residues: 549 sheet: 0.01 (0.35), residues: 234 loop : -0.90 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 58 HIS 0.004 0.001 HIS N 249 PHE 0.010 0.001 PHE N 229 TYR 0.021 0.001 TYR H 41 ARG 0.003 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 131 time to evaluate : 1.204 Fit side-chains REVERT: A 59 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.6974 (pp20) REVERT: B 79 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7854 (mttt) REVERT: C 91 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: D 77 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: E 49 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.6330 (ptp90) REVERT: H 69 ASP cc_start: 0.8473 (t70) cc_final: 0.8219 (t0) REVERT: K 57 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.7923 (mm110) REVERT: K 103 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.6069 (tpt) REVERT: K 111 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7957 (pp20) REVERT: K 219 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7930 (mtm-85) REVERT: N 23 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: N 163 THR cc_start: 0.8685 (m) cc_final: 0.8410 (p) REVERT: N 176 ARG cc_start: 0.7151 (ttm110) cc_final: 0.6654 (mtp180) outliers start: 46 outliers final: 22 residues processed: 160 average time/residue: 1.5908 time to fit residues: 275.7694 Evaluate side-chains 159 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 57 GLN Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 219 ARG Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 239 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16529 Z= 0.177 Angle : 0.541 7.623 23618 Z= 0.320 Chirality : 0.034 0.142 2663 Planarity : 0.003 0.048 1949 Dihedral : 29.467 155.031 4680 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.11 % Allowed : 24.27 % Favored : 71.62 % 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: 1.38 (0.25), residues: 1186 helix: 2.49 (0.22), residues: 545 sheet: 0.15 (0.35), residues: 234 loop : -0.81 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 58 HIS 0.004 0.001 HIS N 249 PHE 0.008 0.001 PHE N 229 TYR 0.013 0.001 TYR N 72 ARG 0.003 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 138 time to evaluate : 1.399 Fit side-chains REVERT: C 91 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: D 77 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: E 49 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.6595 (ptp90) REVERT: E 120 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7618 (mtt) REVERT: G 64 GLU cc_start: 0.7889 (tt0) cc_final: 0.7682 (tp30) REVERT: G 91 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: H 69 ASP cc_start: 0.8244 (t70) cc_final: 0.7958 (t0) REVERT: K 57 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.7792 (mm110) REVERT: K 65 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8262 (mm-40) REVERT: K 103 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.6032 (tpt) REVERT: K 111 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7864 (pp20) REVERT: N 163 THR cc_start: 0.8489 (m) cc_final: 0.8260 (p) outliers start: 42 outliers final: 16 residues processed: 163 average time/residue: 1.5216 time to fit residues: 269.0048 Evaluate side-chains 155 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 57 GLN Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 239 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 138 optimal weight: 0.0020 chunk 114 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16529 Z= 0.168 Angle : 0.547 10.501 23618 Z= 0.321 Chirality : 0.034 0.198 2663 Planarity : 0.003 0.044 1949 Dihedral : 29.463 155.179 4679 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.62 % Allowed : 24.56 % Favored : 71.82 % 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: 1.55 (0.25), residues: 1186 helix: 2.63 (0.22), residues: 545 sheet: 0.22 (0.35), residues: 234 loop : -0.73 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 58 HIS 0.004 0.001 HIS H 50 PHE 0.007 0.001 PHE N 229 TYR 0.016 0.001 TYR N 72 ARG 0.004 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 1.655 Fit side-chains REVERT: B 79 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7979 (mttp) REVERT: C 91 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: D 77 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.6941 (tm-30) REVERT: E 49 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.6307 (ptp90) REVERT: E 120 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7605 (mtt) REVERT: G 64 GLU cc_start: 0.7885 (tt0) cc_final: 0.7671 (tp30) REVERT: G 91 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: H 69 ASP cc_start: 0.8245 (t70) cc_final: 0.7958 (t0) REVERT: K 57 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.7791 (mm110) REVERT: K 65 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8213 (mm-40) REVERT: K 103 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.6027 (tpt) REVERT: K 111 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7865 (pp20) outliers start: 37 outliers final: 19 residues processed: 153 average time/residue: 1.5878 time to fit residues: 264.1417 Evaluate side-chains 157 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 57 GLN Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 239 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16529 Z= 0.177 Angle : 0.544 7.820 23618 Z= 0.320 Chirality : 0.034 0.142 2663 Planarity : 0.003 0.042 1949 Dihedral : 29.446 155.108 4679 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.33 % Allowed : 24.66 % Favored : 72.02 % 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: 1.62 (0.25), residues: 1186 helix: 2.65 (0.22), residues: 549 sheet: 0.27 (0.36), residues: 234 loop : -0.67 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 58 HIS 0.004 0.001 HIS H 50 PHE 0.008 0.001 PHE N 229 TYR 0.015 0.001 TYR N 72 ARG 0.005 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 1.238 Fit side-chains REVERT: A 59 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6938 (pp20) REVERT: B 79 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7985 (mttp) REVERT: C 13 LYS cc_start: 0.5777 (mmmt) cc_final: 0.5018 (mppt) REVERT: C 91 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: D 77 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: E 49 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.6286 (ptp90) REVERT: E 120 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7638 (mtt) REVERT: G 91 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: H 69 ASP cc_start: 0.8304 (t70) cc_final: 0.8028 (t0) REVERT: K 57 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.7733 (mm110) REVERT: K 65 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8230 (mm-40) REVERT: K 103 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.5970 (tpt) outliers start: 34 outliers final: 18 residues processed: 150 average time/residue: 1.5728 time to fit residues: 255.6877 Evaluate side-chains 152 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 57 GLN Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 239 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16529 Z= 0.338 Angle : 0.622 11.026 23618 Z= 0.357 Chirality : 0.039 0.203 2663 Planarity : 0.004 0.043 1949 Dihedral : 29.756 156.974 4679 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.72 % Allowed : 24.66 % Favored : 71.62 % 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: 1.29 (0.25), residues: 1186 helix: 2.25 (0.22), residues: 549 sheet: 0.25 (0.34), residues: 256 loop : -0.77 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 58 HIS 0.007 0.001 HIS H 50 PHE 0.010 0.002 PHE N 229 TYR 0.020 0.002 TYR N 72 ARG 0.007 0.000 ARG N 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 1.268 Fit side-chains REVERT: A 59 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7061 (pp20) REVERT: B 79 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8022 (mttp) REVERT: C 91 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: D 77 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: E 49 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.6214 (ptp90) REVERT: E 120 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.7866 (mtt) REVERT: G 64 GLU cc_start: 0.7917 (tt0) cc_final: 0.7671 (tp30) REVERT: G 91 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: H 69 ASP cc_start: 0.8563 (t70) cc_final: 0.8268 (t0) REVERT: H 87 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7056 (mtt90) REVERT: K 57 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.7915 (mm110) REVERT: K 65 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8261 (mm-40) REVERT: K 103 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.5997 (tpt) REVERT: K 219 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7919 (mtm-85) REVERT: N 57 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7486 (mm110) outliers start: 38 outliers final: 22 residues processed: 147 average time/residue: 1.7677 time to fit residues: 280.8802 Evaluate side-chains 158 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 57 GLN Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 219 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 57 GLN Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 239 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16529 Z= 0.250 Angle : 0.598 10.257 23618 Z= 0.347 Chirality : 0.037 0.208 2663 Planarity : 0.004 0.042 1949 Dihedral : 29.740 156.414 4679 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.91 % Allowed : 24.85 % 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: 1.29 (0.25), residues: 1186 helix: 2.25 (0.22), residues: 549 sheet: 0.24 (0.34), residues: 256 loop : -0.77 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 58 HIS 0.005 0.001 HIS H 50 PHE 0.008 0.001 PHE N 229 TYR 0.017 0.001 TYR N 72 ARG 0.007 0.000 ARG N 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 124 time to evaluate : 1.320 Fit side-chains REVERT: A 59 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7047 (pp20) REVERT: B 79 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8005 (mttp) REVERT: C 91 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: D 77 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.6850 (tm-30) REVERT: E 49 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.6239 (ptp90) REVERT: E 120 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7830 (mtt) REVERT: G 64 GLU cc_start: 0.7909 (tt0) cc_final: 0.7662 (tp30) REVERT: G 91 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: H 69 ASP cc_start: 0.8538 (t70) cc_final: 0.8257 (t0) REVERT: H 87 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7010 (mtt90) REVERT: K 57 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.7900 (mm110) REVERT: K 65 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8257 (mm-40) REVERT: K 103 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.6015 (tpt) REVERT: K 219 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8107 (mtm-85) REVERT: N 176 ARG cc_start: 0.7032 (ttm110) cc_final: 0.6575 (mtp180) outliers start: 40 outliers final: 23 residues processed: 147 average time/residue: 1.6237 time to fit residues: 258.6649 Evaluate side-chains 158 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 57 GLN Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 219 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 239 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16529 Z= 0.265 Angle : 0.587 9.803 23618 Z= 0.341 Chirality : 0.037 0.218 2663 Planarity : 0.004 0.042 1949 Dihedral : 29.631 155.715 4679 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.33 % Allowed : 25.44 % 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: 1.37 (0.25), residues: 1186 helix: 2.37 (0.22), residues: 545 sheet: 0.28 (0.34), residues: 256 loop : -0.79 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 58 HIS 0.006 0.001 HIS H 50 PHE 0.009 0.001 PHE N 229 TYR 0.017 0.001 TYR N 72 ARG 0.007 0.000 ARG N 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.393 Fit side-chains REVERT: A 59 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7017 (pp20) REVERT: B 79 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7887 (mttt) REVERT: C 91 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: D 77 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.6828 (tm-30) REVERT: E 49 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.6303 (ptp90) REVERT: E 120 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.7828 (mtt) REVERT: G 64 GLU cc_start: 0.7911 (tt0) cc_final: 0.7659 (tp30) REVERT: G 91 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: H 69 ASP cc_start: 0.8439 (t70) cc_final: 0.8133 (t0) REVERT: H 87 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7006 (mtt90) REVERT: K 57 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.7788 (mm110) REVERT: K 65 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8312 (mm-40) REVERT: K 103 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.5985 (tpt) outliers start: 34 outliers final: 21 residues processed: 144 average time/residue: 1.5788 time to fit residues: 246.7752 Evaluate side-chains 156 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 57 GLN Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 239 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 104 optimal weight: 0.0970 chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 116 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.138620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.099157 restraints weight = 22543.288| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.70 r_work: 0.3357 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16529 Z= 0.171 Angle : 0.578 9.411 23618 Z= 0.338 Chirality : 0.035 0.209 2663 Planarity : 0.004 0.041 1949 Dihedral : 29.642 155.873 4679 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.42 % Allowed : 25.34 % 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: 1186 helix: 2.53 (0.22), residues: 545 sheet: 0.27 (0.34), residues: 256 loop : -0.74 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 58 HIS 0.005 0.001 HIS H 50 PHE 0.007 0.001 PHE N 229 TYR 0.013 0.001 TYR N 72 ARG 0.009 0.000 ARG N 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5127.47 seconds wall clock time: 92 minutes 15.21 seconds (5535.21 seconds total)