Starting phenix.real_space_refine on Wed Feb 14 01:53:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fje_31619/02_2024/7fje_31619_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fje_31619/02_2024/7fje_31619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fje_31619/02_2024/7fje_31619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fje_31619/02_2024/7fje_31619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fje_31619/02_2024/7fje_31619_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fje_31619/02_2024/7fje_31619_updated.pdb" } resolution = 3.0 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= -0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5322 2.51 5 N 1370 2.21 5 O 1592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a ARG 52": "NH1" <-> "NH2" Residue "d ARG 72": "NH1" <-> "NH2" Residue "e ARG 115": "NH1" <-> "NH2" Residue "f ARG 155": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m ARG 185": "NH1" <-> "NH2" Residue "m ARG 253": "NH1" <-> "NH2" Residue "m ARG 269": "NH1" <-> "NH2" Residue "n PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 228": "NH1" <-> "NH2" Residue "n ARG 246": "NH1" <-> "NH2" 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: 8338 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 264 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "b" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "d" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "e" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "f" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 949 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "g" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "m" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1924 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 233} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2240 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.64, per 1000 atoms: 0.56 Number of scatterers: 8338 At special positions: 0 Unit cell: (92.4, 97.9, 139.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1592 8.00 N 1370 7.00 C 5322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.02 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.04 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.04 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 111 " distance=2.04 Simple disulfide: pdb=" SG CYS m 155 " - pdb=" SG CYS m 205 " distance=2.03 Simple disulfide: pdb=" SG CYS m 227 " - pdb=" SG CYS n 264 " distance=2.03 Simple disulfide: pdb=" SG CYS n 42 " - pdb=" SG CYS n 110 " distance=2.04 Simple disulfide: pdb=" SG CYS n 164 " - pdb=" SG CYS n 229 " 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: 3.14 Conformation dependent library (CDL) restraints added in 1.5 seconds 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 19 sheets defined 22.8% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'a' and resid 29 through 53 removed outlier: 4.075A pdb=" N LEU a 39 " --> pdb=" O LEU a 35 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 50 removed outlier: 3.634A pdb=" N ILE b 38 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU b 39 " --> pdb=" O LEU b 35 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE b 40 " --> pdb=" O ASP b 36 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 65 No H-bonds generated for 'chain 'd' and resid 63 through 65' Processing helix chain 'd' and resid 103 through 123 removed outlier: 4.136A pdb=" N PHE d 123 " --> pdb=" O ALA d 119 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 107 No H-bonds generated for 'chain 'e' and resid 105 through 107' Processing helix chain 'e' and resid 128 through 153 Processing helix chain 'f' and resid 129 through 153 removed outlier: 4.525A pdb=" N GLY f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU f 144 " --> pdb=" O ILE f 140 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU f 145 " --> pdb=" O THR f 141 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU f 146 " --> pdb=" O GLY f 142 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 79 No H-bonds generated for 'chain 'g' and resid 77 through 79' Processing helix chain 'g' and resid 112 through 137 Processing helix chain 'm' and resid 103 through 105 No H-bonds generated for 'chain 'm' and resid 103 through 105' Processing helix chain 'm' and resid 232 through 234 No H-bonds generated for 'chain 'm' and resid 232 through 234' Processing helix chain 'm' and resid 240 through 272 removed outlier: 3.648A pdb=" N ILE m 254 " --> pdb=" O ILE m 250 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU m 268 " --> pdb=" O LEU m 264 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG m 269 " --> pdb=" O LEU m 265 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU m 270 " --> pdb=" O MET m 266 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP m 271 " --> pdb=" O THR m 267 " (cutoff:3.500A) Processing helix chain 'n' and resid 136 through 138 No H-bonds generated for 'chain 'n' and resid 136 through 138' Processing helix chain 'n' and resid 151 through 156 Processing helix chain 'n' and resid 217 through 220 No H-bonds generated for 'chain 'n' and resid 217 through 220' Processing helix chain 'n' and resid 271 through 306 Processing sheet with id= A, first strand: chain 'd' and resid 25 through 27 Processing sheet with id= B, first strand: chain 'd' and resid 83 through 89 removed outlier: 4.027A pdb=" N SER d 84 " --> pdb=" O CYS d 73 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU d 45 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG d 72 " --> pdb=" O TRP d 43 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TRP d 43 " --> pdb=" O ARG d 72 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'e' and resid 37 through 40 removed outlier: 3.785A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU e 82 " --> pdb=" O LEU e 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER e 83 " --> pdb=" O GLY e 76 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'e' and resid 57 through 61 removed outlier: 3.506A pdb=" N TYR e 99 " --> pdb=" O LEU e 58 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'f' and resid 37 through 40 Processing sheet with id= F, first strand: chain 'f' and resid 64 through 66 removed outlier: 3.626A pdb=" N ILE f 66 " --> pdb=" O TRP f 59 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TRP f 59 " --> pdb=" O ILE f 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.582A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'g' and resid 97 through 100 removed outlier: 3.626A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP g 55 " --> pdb=" O GLY g 63 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY g 63 " --> pdb=" O TRP g 55 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LYS g 57 " --> pdb=" O MET g 61 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N MET g 61 " --> pdb=" O LYS g 57 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'm' and resid 33 through 36 Processing sheet with id= J, first strand: chain 'm' and resid 40 through 45 removed outlier: 3.510A pdb=" N TYR m 93 " --> pdb=" O ASP m 88 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'm' and resid 108 through 114 removed outlier: 3.518A pdb=" N TYR m 54 " --> pdb=" O SER m 114 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET m 70 " --> pdb=" O TRP m 57 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG m 59 " --> pdb=" O LEU m 68 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU m 68 " --> pdb=" O ARG m 59 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'm' and resid 140 through 143 removed outlier: 3.859A pdb=" N ALA m 140 " --> pdb=" O THR m 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'm' and resid 180 through 184 Processing sheet with id= N, first strand: chain 'n' and resid 23 through 26 Processing sheet with id= O, first strand: chain 'n' and resid 29 through 32 removed outlier: 6.474A pdb=" N ARG n 129 " --> pdb=" O GLN n 30 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU n 32 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR n 131 " --> pdb=" O LEU n 32 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'n' and resid 38 through 40 removed outlier: 3.925A pdb=" N SER n 86 " --> pdb=" O PRO n 94 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'n' and resid 107 through 112 removed outlier: 3.821A pdb=" N VAL n 107 " --> pdb=" O GLN n 56 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA n 111 " --> pdb=" O SER n 52 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET n 51 " --> pdb=" O SER n 68 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS n 66 " --> pdb=" O TRP n 53 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG n 55 " --> pdb=" O LEU n 64 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU n 64 " --> pdb=" O ARG n 55 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASP n 57 " --> pdb=" O LEU n 62 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU n 62 " --> pdb=" O ASP n 57 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'n' and resid 143 through 147 removed outlier: 5.520A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER n 190 " --> pdb=" O ARG n 212 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'n' and resid 175 through 180 310 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2553 1.34 - 1.47: 2224 1.47 - 1.60: 3666 1.60 - 1.73: 0 1.73 - 1.86: 76 Bond restraints: 8519 Sorted by residual: bond pdb=" CA TYR d 79 " pdb=" C TYR d 79 " ideal model delta sigma weight residual 1.523 1.586 -0.063 1.34e-02 5.57e+03 2.20e+01 bond pdb=" C SER e 103 " pdb=" N LYS e 104 " ideal model delta sigma weight residual 1.327 1.233 0.094 2.86e-02 1.22e+03 1.09e+01 bond pdb=" CA SER m 235 " pdb=" CB SER m 235 " ideal model delta sigma weight residual 1.531 1.434 0.097 3.12e-02 1.03e+03 9.61e+00 bond pdb=" CG LEU f 114 " pdb=" CD2 LEU f 114 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.97e+00 bond pdb=" CB ARG n 228 " pdb=" CG ARG n 228 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.63e+00 ... (remaining 8514 not shown) Histogram of bond angle deviations from ideal: 98.96 - 106.01: 186 106.01 - 113.06: 4487 113.06 - 120.11: 3160 120.11 - 127.16: 3631 127.16 - 134.21: 94 Bond angle restraints: 11558 Sorted by residual: angle pdb=" N ILE d 78 " pdb=" CA ILE d 78 " pdb=" C ILE d 78 " ideal model delta sigma weight residual 109.34 125.08 -15.74 2.08e+00 2.31e-01 5.73e+01 angle pdb=" C PHE m 160 " pdb=" N ASP m 161 " pdb=" CA ASP m 161 " ideal model delta sigma weight residual 121.54 133.08 -11.54 1.91e+00 2.74e-01 3.65e+01 angle pdb=" CA TYR d 79 " pdb=" C TYR d 79 " pdb=" O TYR d 79 " ideal model delta sigma weight residual 120.51 113.15 7.36 1.43e+00 4.89e-01 2.65e+01 angle pdb=" C LYS g 79 " pdb=" N ASP g 80 " pdb=" CA ASP g 80 " ideal model delta sigma weight residual 121.80 134.21 -12.41 2.44e+00 1.68e-01 2.59e+01 angle pdb=" C GLU g 67 " pdb=" N ASP g 68 " pdb=" CA ASP g 68 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 ... (remaining 11553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 4828 16.48 - 32.97: 228 32.97 - 49.45: 89 49.45 - 65.93: 9 65.93 - 82.42: 8 Dihedral angle restraints: 5162 sinusoidal: 2086 harmonic: 3076 Sorted by residual: dihedral pdb=" CA GLU n 49 " pdb=" C GLU n 49 " pdb=" N TYR n 50 " pdb=" CA TYR n 50 " ideal model delta harmonic sigma weight residual 180.00 127.66 52.34 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA ASP d 77 " pdb=" C ASP d 77 " pdb=" N ILE d 78 " pdb=" CA ILE d 78 " ideal model delta harmonic sigma weight residual -180.00 -131.28 -48.72 0 5.00e+00 4.00e-02 9.49e+01 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual -86.00 -168.42 82.42 1 1.00e+01 1.00e-02 8.33e+01 ... (remaining 5159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1071 0.086 - 0.173: 212 0.173 - 0.259: 13 0.259 - 0.346: 2 0.346 - 0.432: 1 Chirality restraints: 1299 Sorted by residual: chirality pdb=" CB ILE m 134 " pdb=" CA ILE m 134 " pdb=" CG1 ILE m 134 " pdb=" CG2 ILE m 134 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CA ASP g 80 " pdb=" N ASP g 80 " pdb=" C ASP g 80 " pdb=" CB ASP g 80 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CG LEU a 27 " pdb=" CB LEU a 27 " pdb=" CD1 LEU a 27 " pdb=" CD2 LEU a 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1296 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR e 111 " -0.019 2.00e-02 2.50e+03 2.10e-02 8.85e+00 pdb=" CG TYR e 111 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR e 111 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR e 111 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR e 111 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR e 111 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR e 111 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR e 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 90 " -0.021 2.00e-02 2.50e+03 2.03e-02 8.26e+00 pdb=" CG TYR d 90 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR d 90 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR d 90 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR d 90 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR d 90 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR d 90 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR d 90 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN n 194 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.75e+00 pdb=" N PRO n 195 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO n 195 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO n 195 " 0.033 5.00e-02 4.00e+02 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2178 2.81 - 3.33: 6478 3.33 - 3.85: 12263 3.85 - 4.38: 13294 4.38 - 4.90: 24306 Nonbonded interactions: 58519 Sorted by model distance: nonbonded pdb=" OG SER m 118 " pdb=" OE1 GLN n 116 " model vdw 2.287 2.440 nonbonded pdb=" N ASP m 159 " pdb=" OD1 ASP m 159 " model vdw 2.391 2.520 nonbonded pdb=" OG SER a 23 " pdb=" OE1 GLN d 94 " model vdw 2.405 2.440 nonbonded pdb=" O TYR m 71 " pdb=" NZ LYS m 78 " model vdw 2.441 2.520 nonbonded pdb=" O PHE a 24 " pdb=" OG1 THR m 238 " model vdw 2.451 2.440 ... (remaining 58514 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 26 through 54) selection = (chain 'b' and resid 26 through 54) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 155)) selection = (chain 'f' and resid 33 through 155) } 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: 0.890 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: 4.000 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 24.840 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.010 0.109 8519 Z= 0.635 Angle : 1.192 16.314 11558 Z= 0.641 Chirality : 0.066 0.432 1299 Planarity : 0.008 0.060 1468 Dihedral : 11.624 76.759 3149 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.88 % Favored : 91.83 % Rotamer: Outliers : 0.97 % Allowed : 5.62 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.80 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.22), residues: 1040 helix: -0.57 (0.31), residues: 231 sheet: -1.05 (0.32), residues: 234 loop : -3.21 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP m 197 HIS 0.016 0.004 HIS f 61 PHE 0.036 0.004 PHE n 29 TYR 0.051 0.005 TYR e 111 ARG 0.010 0.001 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 224 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8289 (tppp) cc_final: 0.7567 (tmmm) REVERT: d 117 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7575 (tp) REVERT: e 85 LYS cc_start: 0.8689 (mttt) cc_final: 0.8482 (mmmm) REVERT: e 103 SER cc_start: 0.9035 (t) cc_final: 0.8765 (m) REVERT: e 121 ASN cc_start: 0.7809 (m110) cc_final: 0.7365 (m-40) REVERT: e 124 GLU cc_start: 0.8648 (tt0) cc_final: 0.8444 (tt0) REVERT: e 128 MET cc_start: 0.7390 (mmm) cc_final: 0.6975 (mmt) REVERT: f 51 GLN cc_start: 0.8306 (mt0) cc_final: 0.8041 (mp10) REVERT: f 104 LYS cc_start: 0.9093 (mttt) cc_final: 0.8807 (mmmt) REVERT: f 127 VAL cc_start: 0.8708 (m) cc_final: 0.8478 (p) REVERT: m 188 ASP cc_start: 0.7712 (t0) cc_final: 0.7380 (t70) REVERT: n 33 LYS cc_start: 0.8759 (ttpt) cc_final: 0.8136 (tttt) REVERT: n 121 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6868 (tt0) REVERT: n 135 ASP cc_start: 0.8430 (t70) cc_final: 0.8166 (t0) outliers start: 9 outliers final: 1 residues processed: 227 average time/residue: 1.0373 time to fit residues: 251.8428 Evaluate side-chains 147 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.0370 chunk 79 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 36 ASN f 62 ASN f 65 ASN f 74 ASN f 121 ASN g 29 HIS g 37 GLN m 86 GLN n 25 GLN n 47 ASN n 273 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8519 Z= 0.170 Angle : 0.649 8.946 11558 Z= 0.339 Chirality : 0.044 0.201 1299 Planarity : 0.005 0.047 1468 Dihedral : 6.420 59.491 1212 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.38 % Favored : 94.52 % Rotamer: Outliers : 3.56 % Allowed : 13.61 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.34 (0.25), residues: 1040 helix: 2.40 (0.33), residues: 224 sheet: 0.05 (0.32), residues: 264 loop : -3.00 (0.21), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP m 197 HIS 0.003 0.001 HIS g 29 PHE 0.018 0.001 PHE m 157 TYR 0.022 0.002 TYR g 34 ARG 0.003 0.000 ARG m 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: b 46 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8222 (mt) REVERT: b 54 LYS cc_start: 0.8299 (tppp) cc_final: 0.7578 (tmmm) REVERT: d 29 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7608 (mp) REVERT: e 37 LYS cc_start: 0.8002 (mmtp) cc_final: 0.7686 (mttm) REVERT: e 103 SER cc_start: 0.8960 (t) cc_final: 0.8693 (m) REVERT: e 104 LYS cc_start: 0.8935 (mtpm) cc_final: 0.8628 (mttp) REVERT: e 120 GLU cc_start: 0.7650 (tp30) cc_final: 0.7448 (tp30) REVERT: e 121 ASN cc_start: 0.7958 (m110) cc_final: 0.7293 (m-40) REVERT: e 124 GLU cc_start: 0.8566 (tt0) cc_final: 0.8322 (tt0) REVERT: e 128 MET cc_start: 0.6815 (mmm) cc_final: 0.6500 (mmt) REVERT: f 56 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7724 (mm-30) REVERT: f 74 ASN cc_start: 0.5620 (OUTLIER) cc_final: 0.5398 (p0) REVERT: f 104 LYS cc_start: 0.9024 (mttt) cc_final: 0.8752 (mmmt) REVERT: g 64 PHE cc_start: 0.7409 (t80) cc_final: 0.6812 (t80) REVERT: m 53 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7829 (pt0) REVERT: m 71 TYR cc_start: 0.6779 (t80) cc_final: 0.5058 (t80) REVERT: m 188 ASP cc_start: 0.7811 (t0) cc_final: 0.7525 (t70) REVERT: n 33 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8258 (tttt) REVERT: n 121 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6704 (mp0) outliers start: 33 outliers final: 15 residues processed: 201 average time/residue: 0.9862 time to fit residues: 212.9258 Evaluate side-chains 163 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 74 ASN Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 90 SER Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 245 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 62 ASN f 74 ASN g 37 GLN m 168 GLN m 211 ASN ** n 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8519 Z= 0.210 Angle : 0.631 8.795 11558 Z= 0.331 Chirality : 0.044 0.202 1299 Planarity : 0.004 0.045 1468 Dihedral : 5.881 57.433 1208 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.83 % Favored : 92.98 % Rotamer: Outliers : 4.86 % Allowed : 15.77 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.26), residues: 1040 helix: 3.28 (0.32), residues: 225 sheet: 0.58 (0.33), residues: 264 loop : -2.83 (0.21), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP n 259 HIS 0.003 0.001 HIS g 29 PHE 0.014 0.002 PHE e 110 TYR 0.021 0.002 TYR g 34 ARG 0.004 0.000 ARG f 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 149 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8349 (tppp) cc_final: 0.7592 (tmmm) REVERT: d 29 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7585 (mp) REVERT: e 37 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7911 (mttm) REVERT: e 103 SER cc_start: 0.8975 (t) cc_final: 0.8717 (m) REVERT: e 104 LYS cc_start: 0.8936 (mtpm) cc_final: 0.8621 (mtmp) REVERT: e 121 ASN cc_start: 0.7900 (m110) cc_final: 0.7167 (m-40) REVERT: e 124 GLU cc_start: 0.8607 (tt0) cc_final: 0.8362 (tt0) REVERT: e 128 MET cc_start: 0.6903 (mmm) cc_final: 0.6581 (mmt) REVERT: f 56 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: f 104 LYS cc_start: 0.9069 (mttt) cc_final: 0.8766 (mmmt) REVERT: f 125 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7000 (mmm) REVERT: f 128 MET cc_start: 0.7016 (ttt) cc_final: 0.6679 (tpt) REVERT: f 135 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7791 (mp) REVERT: f 140 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7575 (mp) REVERT: g 105 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6587 (tm-30) REVERT: m 53 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7678 (pt0) REVERT: m 188 ASP cc_start: 0.7826 (t0) cc_final: 0.7545 (t70) REVERT: m 211 ASN cc_start: 0.8753 (t0) cc_final: 0.8444 (t0) REVERT: n 33 LYS cc_start: 0.8917 (ttpt) cc_final: 0.8597 (ttmm) REVERT: n 113 ARG cc_start: 0.7874 (mtp180) cc_final: 0.7586 (mtp-110) REVERT: n 121 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6832 (tt0) outliers start: 45 outliers final: 26 residues processed: 177 average time/residue: 1.0792 time to fit residues: 204.5942 Evaluate side-chains 172 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 74 ASN Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain f residue 125 MET Chi-restraints excluded: chain f residue 135 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 82 ARG Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 267 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 245 ASP Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0970 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 51 GLN f 74 ASN ** n 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8519 Z= 0.189 Angle : 0.598 8.476 11558 Z= 0.313 Chirality : 0.043 0.201 1299 Planarity : 0.004 0.042 1468 Dihedral : 5.563 52.581 1208 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.35 % Favored : 93.56 % Rotamer: Outliers : 5.40 % Allowed : 17.60 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.41 (0.26), residues: 1040 helix: 3.74 (0.31), residues: 223 sheet: 0.72 (0.33), residues: 266 loop : -2.74 (0.22), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP n 259 HIS 0.003 0.001 HIS n 226 PHE 0.015 0.001 PHE m 55 TYR 0.026 0.002 TYR m 93 ARG 0.004 0.000 ARG f 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 144 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8366 (tppp) cc_final: 0.7581 (tmmm) REVERT: d 29 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7550 (mp) REVERT: e 37 LYS cc_start: 0.8098 (mmtp) cc_final: 0.7887 (mttm) REVERT: e 103 SER cc_start: 0.9021 (t) cc_final: 0.8735 (m) REVERT: e 104 LYS cc_start: 0.8938 (mtpm) cc_final: 0.8624 (mtmp) REVERT: e 120 GLU cc_start: 0.7727 (tp30) cc_final: 0.7509 (tp30) REVERT: e 121 ASN cc_start: 0.7908 (m110) cc_final: 0.7144 (m-40) REVERT: e 124 GLU cc_start: 0.8593 (tt0) cc_final: 0.8333 (tt0) REVERT: e 128 MET cc_start: 0.6865 (mmm) cc_final: 0.6549 (mmt) REVERT: f 56 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7677 (mm-30) REVERT: f 74 ASN cc_start: 0.4962 (OUTLIER) cc_final: 0.4761 (p0) REVERT: f 104 LYS cc_start: 0.9059 (mttt) cc_final: 0.8752 (mmmt) REVERT: f 125 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7063 (mmm) REVERT: f 128 MET cc_start: 0.7131 (ttt) cc_final: 0.6710 (tpt) REVERT: f 135 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7770 (mp) REVERT: f 140 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7628 (mp) REVERT: g 51 LYS cc_start: 0.7653 (tppt) cc_final: 0.7322 (tppt) REVERT: g 105 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6604 (tm-30) REVERT: m 53 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7581 (pt0) REVERT: m 188 ASP cc_start: 0.7799 (t0) cc_final: 0.7519 (t70) REVERT: m 211 ASN cc_start: 0.8784 (t0) cc_final: 0.8378 (t0) REVERT: n 33 LYS cc_start: 0.8927 (ttpt) cc_final: 0.8607 (ttmm) REVERT: n 121 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6796 (tt0) outliers start: 50 outliers final: 29 residues processed: 180 average time/residue: 1.0675 time to fit residues: 205.6773 Evaluate side-chains 172 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 135 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 74 ASN Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain f residue 125 MET Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 135 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 82 ARG Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 267 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 245 ASP Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 294 VAL Chi-restraints excluded: chain n residue 296 VAL Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 74 ASN g 52 ASN n 25 GLN ** n 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8519 Z= 0.192 Angle : 0.596 9.055 11558 Z= 0.311 Chirality : 0.043 0.192 1299 Planarity : 0.004 0.038 1468 Dihedral : 5.422 52.905 1208 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.54 % Favored : 93.27 % Rotamer: Outliers : 5.62 % Allowed : 17.39 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.20 (0.26), residues: 1040 helix: 3.90 (0.31), residues: 224 sheet: 0.91 (0.33), residues: 266 loop : -2.64 (0.22), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP n 259 HIS 0.003 0.001 HIS n 226 PHE 0.018 0.001 PHE g 64 TYR 0.022 0.002 TYR g 34 ARG 0.004 0.000 ARG f 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 141 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: b 35 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8915 (mt) REVERT: b 54 LYS cc_start: 0.8376 (tppp) cc_final: 0.7579 (tmmm) REVERT: d 29 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7525 (mp) REVERT: e 37 LYS cc_start: 0.8126 (mmtp) cc_final: 0.7911 (mttm) REVERT: e 103 SER cc_start: 0.8990 (t) cc_final: 0.8724 (m) REVERT: e 104 LYS cc_start: 0.8937 (mtpm) cc_final: 0.8638 (mtmp) REVERT: e 115 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7710 (ttm-80) REVERT: e 124 GLU cc_start: 0.8561 (tt0) cc_final: 0.8289 (tt0) REVERT: e 128 MET cc_start: 0.6865 (mmm) cc_final: 0.6546 (mmt) REVERT: f 56 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7688 (mm-30) REVERT: f 104 LYS cc_start: 0.9034 (mttt) cc_final: 0.8743 (mmmt) REVERT: f 128 MET cc_start: 0.7084 (ttt) cc_final: 0.6736 (tpt) REVERT: f 135 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7771 (mp) REVERT: f 140 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7676 (mp) REVERT: g 51 LYS cc_start: 0.7532 (tppt) cc_final: 0.7292 (tppt) REVERT: g 105 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6633 (tm-30) REVERT: m 53 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7524 (pt0) REVERT: m 188 ASP cc_start: 0.7797 (t0) cc_final: 0.7537 (t70) REVERT: m 211 ASN cc_start: 0.8789 (t0) cc_final: 0.8379 (t0) REVERT: n 33 LYS cc_start: 0.8926 (ttpt) cc_final: 0.8625 (ttmm) REVERT: n 121 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6901 (tt0) outliers start: 52 outliers final: 26 residues processed: 176 average time/residue: 1.0283 time to fit residues: 194.5292 Evaluate side-chains 170 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 135 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 67 GLU Chi-restraints excluded: chain m residue 82 ARG Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 245 ASP Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 296 VAL Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 0.0040 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 0.0370 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.4270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 61 HIS e 121 ASN n 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8519 Z= 0.132 Angle : 0.549 8.697 11558 Z= 0.287 Chirality : 0.041 0.180 1299 Planarity : 0.003 0.034 1468 Dihedral : 5.060 54.556 1208 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 4.54 % Allowed : 18.47 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.14 (0.27), residues: 1040 helix: 4.32 (0.30), residues: 221 sheet: 1.02 (0.33), residues: 280 loop : -2.49 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP m 197 HIS 0.002 0.001 HIS g 29 PHE 0.010 0.001 PHE m 55 TYR 0.031 0.001 TYR m 93 ARG 0.002 0.000 ARG m 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: b 35 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8921 (mt) REVERT: b 54 LYS cc_start: 0.8355 (tppp) cc_final: 0.7581 (tmmm) REVERT: e 37 LYS cc_start: 0.8014 (mmtp) cc_final: 0.7731 (mttm) REVERT: e 103 SER cc_start: 0.8981 (t) cc_final: 0.8740 (m) REVERT: e 124 GLU cc_start: 0.8475 (tt0) cc_final: 0.8195 (tt0) REVERT: e 128 MET cc_start: 0.6653 (mmm) cc_final: 0.6367 (mmt) REVERT: f 56 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: f 104 LYS cc_start: 0.8986 (mttt) cc_final: 0.8709 (mmmt) REVERT: f 123 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7352 (ptp) REVERT: f 128 MET cc_start: 0.6872 (ttt) cc_final: 0.6450 (mmt) REVERT: f 140 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7690 (mp) REVERT: g 105 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6726 (tp40) REVERT: m 53 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7481 (pt0) REVERT: m 70 MET cc_start: 0.7707 (mmm) cc_final: 0.7308 (mmm) REVERT: m 159 ASP cc_start: 0.6260 (OUTLIER) cc_final: 0.5949 (p0) REVERT: m 188 ASP cc_start: 0.7754 (t0) cc_final: 0.7498 (t70) REVERT: m 211 ASN cc_start: 0.8788 (t0) cc_final: 0.8395 (t0) REVERT: n 33 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8568 (ttmm) REVERT: n 40 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7639 (mt) REVERT: n 50 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6451 (p90) REVERT: n 51 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7323 (mmm) outliers start: 42 outliers final: 20 residues processed: 177 average time/residue: 1.1334 time to fit residues: 214.7330 Evaluate side-chains 171 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 93 TYR Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 51 MET Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN n 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8519 Z= 0.200 Angle : 0.607 9.276 11558 Z= 0.312 Chirality : 0.043 0.188 1299 Planarity : 0.004 0.038 1468 Dihedral : 5.195 53.908 1208 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.54 % Favored : 93.37 % Rotamer: Outliers : 4.64 % Allowed : 18.25 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.08 (0.27), residues: 1040 helix: 4.11 (0.30), residues: 228 sheet: 1.04 (0.33), residues: 269 loop : -2.51 (0.22), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP n 259 HIS 0.003 0.001 HIS n 226 PHE 0.014 0.001 PHE g 64 TYR 0.028 0.002 TYR m 93 ARG 0.004 0.000 ARG f 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: b 35 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8914 (mt) REVERT: b 54 LYS cc_start: 0.8371 (tppp) cc_final: 0.7577 (tmmm) REVERT: d 29 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7460 (mp) REVERT: e 37 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7886 (mttm) REVERT: e 103 SER cc_start: 0.8942 (t) cc_final: 0.8667 (m) REVERT: e 104 LYS cc_start: 0.8971 (mtpm) cc_final: 0.8666 (mtmp) REVERT: e 115 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7694 (ttm-80) REVERT: e 124 GLU cc_start: 0.8486 (tt0) cc_final: 0.8210 (tt0) REVERT: e 128 MET cc_start: 0.6854 (mmm) cc_final: 0.6541 (mmt) REVERT: f 56 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7748 (mm-30) REVERT: f 104 LYS cc_start: 0.8982 (mttt) cc_final: 0.8663 (mmmt) REVERT: f 128 MET cc_start: 0.7034 (ttt) cc_final: 0.6500 (mmt) REVERT: f 135 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7746 (mp) REVERT: f 140 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7823 (mp) REVERT: g 105 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6941 (tm-30) REVERT: m 47 TYR cc_start: 0.8347 (p90) cc_final: 0.8107 (p90) REVERT: m 53 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: m 70 MET cc_start: 0.7732 (mmm) cc_final: 0.7399 (mmm) REVERT: m 94 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8415 (pt) REVERT: m 159 ASP cc_start: 0.6481 (OUTLIER) cc_final: 0.6123 (p0) REVERT: m 182 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8207 (pt) REVERT: m 188 ASP cc_start: 0.7797 (t0) cc_final: 0.7523 (t70) REVERT: m 211 ASN cc_start: 0.8812 (t0) cc_final: 0.8388 (t0) REVERT: n 33 LYS cc_start: 0.8925 (ttpt) cc_final: 0.8580 (ttmm) REVERT: n 50 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6432 (p90) REVERT: n 121 GLU cc_start: 0.6785 (tt0) cc_final: 0.6498 (tm-30) outliers start: 43 outliers final: 23 residues processed: 169 average time/residue: 1.0623 time to fit residues: 192.3232 Evaluate side-chains 172 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 74 ASN Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 135 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 67 GLU Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 294 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 94 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 0.0770 chunk 55 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN n 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8519 Z= 0.149 Angle : 0.564 8.810 11558 Z= 0.291 Chirality : 0.042 0.178 1299 Planarity : 0.003 0.033 1468 Dihedral : 4.985 54.773 1208 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 4.10 % Allowed : 19.01 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.36 (0.27), residues: 1040 helix: 4.55 (0.29), residues: 221 sheet: 1.18 (0.33), residues: 277 loop : -2.35 (0.23), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP n 259 HIS 0.002 0.001 HIS n 48 PHE 0.009 0.001 PHE m 55 TYR 0.027 0.001 TYR m 93 ARG 0.002 0.000 ARG f 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: b 35 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8912 (mt) REVERT: b 54 LYS cc_start: 0.8358 (tppp) cc_final: 0.7576 (tmmm) REVERT: d 29 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7418 (mt) REVERT: e 37 LYS cc_start: 0.8058 (mmtp) cc_final: 0.7830 (mttm) REVERT: e 103 SER cc_start: 0.8952 (t) cc_final: 0.8697 (m) REVERT: e 104 LYS cc_start: 0.8972 (mtpm) cc_final: 0.8673 (mtmp) REVERT: e 124 GLU cc_start: 0.8482 (tt0) cc_final: 0.8202 (tt0) REVERT: e 128 MET cc_start: 0.6703 (mmm) cc_final: 0.6410 (mmt) REVERT: f 56 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: f 104 LYS cc_start: 0.8942 (mttt) cc_final: 0.8654 (mmmt) REVERT: f 123 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7379 (ptp) REVERT: f 128 MET cc_start: 0.6926 (ttt) cc_final: 0.6454 (mmt) REVERT: f 140 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7680 (mp) REVERT: g 105 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6577 (tp40) REVERT: g 131 VAL cc_start: 0.8573 (t) cc_final: 0.8348 (t) REVERT: m 53 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7385 (pt0) REVERT: m 70 MET cc_start: 0.7746 (mmm) cc_final: 0.7261 (mmm) REVERT: m 159 ASP cc_start: 0.6261 (OUTLIER) cc_final: 0.5992 (p0) REVERT: m 188 ASP cc_start: 0.7750 (t0) cc_final: 0.7489 (t70) REVERT: m 211 ASN cc_start: 0.8751 (t0) cc_final: 0.8292 (t0) REVERT: n 33 LYS cc_start: 0.8922 (ttpt) cc_final: 0.8576 (ttmm) REVERT: n 50 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6170 (p90) REVERT: n 113 ARG cc_start: 0.7857 (ttp-170) cc_final: 0.7599 (ttm170) REVERT: n 250 VAL cc_start: 0.8748 (m) cc_final: 0.8498 (t) outliers start: 38 outliers final: 22 residues processed: 174 average time/residue: 1.0743 time to fit residues: 200.4415 Evaluate side-chains 172 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 295 LEU Chi-restraints excluded: chain n residue 296 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 163 GLN n 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8519 Z= 0.201 Angle : 0.618 9.849 11558 Z= 0.316 Chirality : 0.043 0.179 1299 Planarity : 0.004 0.038 1468 Dihedral : 5.114 55.501 1208 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.92 % Favored : 92.98 % Rotamer: Outliers : 4.43 % Allowed : 18.57 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.25 (0.27), residues: 1040 helix: 4.31 (0.30), residues: 227 sheet: 1.29 (0.34), residues: 259 loop : -2.43 (0.23), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP n 259 HIS 0.003 0.001 HIS n 226 PHE 0.012 0.001 PHE m 189 TYR 0.028 0.002 TYR m 93 ARG 0.004 0.000 ARG f 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: b 35 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8981 (mt) REVERT: b 46 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8180 (mm) REVERT: b 54 LYS cc_start: 0.8370 (tppp) cc_final: 0.7572 (tmmm) REVERT: d 29 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7451 (mp) REVERT: e 37 LYS cc_start: 0.8141 (mmtp) cc_final: 0.7898 (mttm) REVERT: e 103 SER cc_start: 0.8885 (t) cc_final: 0.8607 (m) REVERT: e 104 LYS cc_start: 0.9006 (mtpm) cc_final: 0.8720 (mtmp) REVERT: e 124 GLU cc_start: 0.8488 (tt0) cc_final: 0.8216 (tt0) REVERT: e 128 MET cc_start: 0.6900 (mmm) cc_final: 0.6572 (mmt) REVERT: f 56 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7717 (mm-30) REVERT: f 104 LYS cc_start: 0.8957 (mttt) cc_final: 0.8639 (mmmt) REVERT: f 128 MET cc_start: 0.7045 (ttt) cc_final: 0.6506 (mmt) REVERT: f 135 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7848 (mp) REVERT: g 105 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6759 (tm-30) REVERT: m 53 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7111 (pt0) REVERT: m 70 MET cc_start: 0.7646 (mmm) cc_final: 0.7306 (mmm) REVERT: m 159 ASP cc_start: 0.6398 (OUTLIER) cc_final: 0.6072 (p0) REVERT: m 182 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8282 (pt) REVERT: m 188 ASP cc_start: 0.7804 (t0) cc_final: 0.7528 (t70) REVERT: m 211 ASN cc_start: 0.8731 (t0) cc_final: 0.8253 (t0) REVERT: n 33 LYS cc_start: 0.8921 (ttpt) cc_final: 0.8565 (ttmm) REVERT: n 50 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6154 (p90) REVERT: n 113 ARG cc_start: 0.7948 (ttp-170) cc_final: 0.7675 (ttm170) outliers start: 41 outliers final: 24 residues processed: 166 average time/residue: 0.9958 time to fit residues: 177.6517 Evaluate side-chains 170 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain f residue 135 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 294 VAL Chi-restraints excluded: chain n residue 296 VAL Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 163 GLN n 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8519 Z= 0.151 Angle : 0.580 8.947 11558 Z= 0.296 Chirality : 0.041 0.170 1299 Planarity : 0.003 0.033 1468 Dihedral : 4.957 56.919 1208 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 3.24 % Allowed : 19.65 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.50 (0.27), residues: 1040 helix: 4.68 (0.29), residues: 221 sheet: 1.34 (0.33), residues: 273 loop : -2.30 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP n 259 HIS 0.002 0.001 HIS n 173 PHE 0.008 0.001 PHE m 55 TYR 0.028 0.001 TYR m 93 ARG 0.003 0.000 ARG n 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: b 35 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8961 (mt) REVERT: b 54 LYS cc_start: 0.8358 (tppp) cc_final: 0.7573 (tmmm) REVERT: d 29 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7386 (mt) REVERT: e 37 LYS cc_start: 0.8066 (mmtp) cc_final: 0.7830 (mttm) REVERT: e 103 SER cc_start: 0.8896 (t) cc_final: 0.8629 (m) REVERT: e 104 LYS cc_start: 0.8968 (mtpm) cc_final: 0.8680 (mtmp) REVERT: e 124 GLU cc_start: 0.8483 (tt0) cc_final: 0.8200 (tt0) REVERT: e 128 MET cc_start: 0.6691 (mmm) cc_final: 0.6401 (mmt) REVERT: f 56 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7686 (mm-30) REVERT: f 104 LYS cc_start: 0.8912 (mttt) cc_final: 0.8634 (mmmt) REVERT: f 123 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7392 (ptp) REVERT: f 128 MET cc_start: 0.6932 (ttt) cc_final: 0.6464 (mmt) REVERT: f 146 LEU cc_start: 0.8154 (tt) cc_final: 0.7605 (mp) REVERT: g 105 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6541 (tp40) REVERT: g 131 VAL cc_start: 0.8578 (t) cc_final: 0.8348 (t) REVERT: m 53 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7107 (pt0) REVERT: m 70 MET cc_start: 0.7639 (mmm) cc_final: 0.7199 (mmm) REVERT: m 159 ASP cc_start: 0.6231 (OUTLIER) cc_final: 0.5988 (p0) REVERT: m 188 ASP cc_start: 0.7743 (t0) cc_final: 0.7474 (t70) REVERT: m 211 ASN cc_start: 0.8681 (t0) cc_final: 0.8239 (t0) REVERT: n 33 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8554 (ttmm) REVERT: n 50 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6312 (p90) outliers start: 30 outliers final: 20 residues processed: 169 average time/residue: 0.9971 time to fit residues: 181.2286 Evaluate side-chains 174 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 295 LEU Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 83 optimal weight: 0.0670 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 163 GLN n 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090628 restraints weight = 11171.764| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.78 r_work: 0.2889 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8519 Z= 0.197 Angle : 0.606 8.940 11558 Z= 0.314 Chirality : 0.043 0.181 1299 Planarity : 0.004 0.042 1468 Dihedral : 5.141 58.282 1208 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.54 % Favored : 93.37 % Rotamer: Outliers : 3.67 % Allowed : 19.33 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.35 (0.27), residues: 1040 helix: 4.39 (0.29), residues: 227 sheet: 1.29 (0.34), residues: 262 loop : -2.35 (0.23), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP n 259 HIS 0.005 0.001 HIS n 48 PHE 0.011 0.001 PHE m 189 TYR 0.019 0.001 TYR b 42 ARG 0.003 0.000 ARG f 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3821.14 seconds wall clock time: 68 minutes 9.62 seconds (4089.62 seconds total)