Starting phenix.real_space_refine on Wed Feb 14 09:16:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvi_35044/02_2024/8hvi_35044_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvi_35044/02_2024/8hvi_35044.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvi_35044/02_2024/8hvi_35044_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvi_35044/02_2024/8hvi_35044_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvi_35044/02_2024/8hvi_35044_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvi_35044/02_2024/8hvi_35044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvi_35044/02_2024/8hvi_35044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvi_35044/02_2024/8hvi_35044_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvi_35044/02_2024/8hvi_35044_neut_updated.pdb" } resolution = 3.04 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= 0.035 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 65 5.16 5 C 5697 2.51 5 N 1537 2.21 5 O 1689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 88": "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: 8988 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2439 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 301} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1713 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 212} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2601 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'NFI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.31, per 1000 atoms: 0.59 Number of scatterers: 8988 At special positions: 0 Unit cell: (115.132, 118.36, 125.892, 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 65 16.00 O 1689 8.00 N 1537 7.00 C 5697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " 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: 3.56 Conformation dependent library (CDL) restraints added in 1.8 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 12 sheets defined 33.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'R' and resid 40 through 71 removed outlier: 3.634A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL R 52 " --> pdb=" O VAL R 48 " (cutoff:3.500A) Proline residue: R 58 - end of helix Processing helix chain 'R' and resid 76 through 90 Processing helix chain 'R' and resid 95 through 101 Processing helix chain 'R' and resid 113 through 145 removed outlier: 3.665A pdb=" N VAL R 117 " --> pdb=" O LEU R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 152 No H-bonds generated for 'chain 'R' and resid 150 through 152' Processing helix chain 'R' and resid 158 through 180 Proline residue: R 176 - end of helix Processing helix chain 'R' and resid 194 through 228 Proline residue: R 211 - end of helix Processing helix chain 'R' and resid 234 through 270 Proline residue: R 257 - end of helix Processing helix chain 'R' and resid 287 through 301 Processing helix chain 'R' and resid 304 through 312 Processing helix chain 'R' and resid 317 through 330 Processing helix chain 'R' and resid 336 through 343 Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.376A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 208 through 211 No H-bonds generated for 'chain 'B' and resid 208 through 211' Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 242 through 254 removed outlier: 3.703A pdb=" N LYS B 248 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 249 " --> pdb=" O GLU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 331 through 351 removed outlier: 4.422A pdb=" N ASP B 337 " --> pdb=" O PHE B 334 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASP B 341 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS B 349 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 30 through 33 Processing helix chain 'D' and resid 9 through 23 removed outlier: 3.655A pdb=" N LYS D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'B' and resid 263 through 267 removed outlier: 4.223A pdb=" N CYS B 224 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N LEU B 36 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS B 197 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU B 38 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE B 199 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLY B 40 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 49 through 52 removed outlier: 4.155A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 338 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 331 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 327 " --> pdb=" O TRP C 339 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.756A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.989A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.774A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER C 161 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 221 through 223 removed outlier: 4.158A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL C 200 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER C 191 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 202 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 251 through 254 Processing sheet with id= H, first strand: chain 'C' and resid 306 through 308 removed outlier: 3.597A pdb=" N ASN C 295 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 17 through 23 removed outlier: 3.592A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 95 through 99 removed outlier: 3.651A pdb=" N TRP H 36 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 128 through 130 Processing sheet with id= L, first strand: chain 'H' and resid 134 through 136 removed outlier: 6.969A pdb=" N LYS H 232 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY H 213 " --> pdb=" O LEU H 233 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL H 214 " --> pdb=" O GLN H 167 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR H 216 " --> pdb=" O PHE H 165 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE H 165 " --> pdb=" O TYR H 216 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1047 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: 2.43 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2745 1.34 - 1.46: 2103 1.46 - 1.58: 4227 1.58 - 1.70: 0 1.70 - 1.83: 90 Bond restraints: 9165 Sorted by residual: bond pdb=" C10 NFI R 401 " pdb=" N1 NFI R 401 " ideal model delta sigma weight residual 1.454 1.349 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C ILE R 210 " pdb=" N PRO R 211 " ideal model delta sigma weight residual 1.335 1.401 -0.066 1.36e-02 5.41e+03 2.35e+01 bond pdb=" N LEU B 348 " pdb=" CA LEU B 348 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.20e-02 6.94e+03 9.62e+00 bond pdb=" C15 NFI R 401 " pdb=" C18 NFI R 401 " ideal model delta sigma weight residual 1.379 1.439 -0.060 2.00e-02 2.50e+03 9.05e+00 bond pdb=" N TYR R 287 " pdb=" CA TYR R 287 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.25e-02 6.40e+03 5.98e+00 ... (remaining 9160 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.48: 111 105.48 - 112.84: 4816 112.84 - 120.21: 3391 120.21 - 127.57: 4006 127.57 - 134.93: 87 Bond angle restraints: 12411 Sorted by residual: angle pdb=" N ILE C 270 " pdb=" CA ILE C 270 " pdb=" C ILE C 270 " ideal model delta sigma weight residual 113.47 107.08 6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C ALA B 338 " pdb=" N VAL B 339 " pdb=" CA VAL B 339 " ideal model delta sigma weight residual 122.35 115.91 6.44 1.18e+00 7.18e-01 2.98e+01 angle pdb=" C17 NFI R 401 " pdb=" C18 NFI R 401 " pdb=" C19 NFI R 401 " ideal model delta sigma weight residual 113.93 128.47 -14.54 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C18 NFI R 401 " pdb=" C17 NFI R 401 " pdb=" C20 NFI R 401 " ideal model delta sigma weight residual 147.07 132.57 14.50 3.00e+00 1.11e-01 2.34e+01 angle pdb=" CB MET H 218 " pdb=" CG MET H 218 " pdb=" SD MET H 218 " ideal model delta sigma weight residual 112.70 125.71 -13.01 3.00e+00 1.11e-01 1.88e+01 ... (remaining 12406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4781 17.94 - 35.87: 516 35.87 - 53.81: 114 53.81 - 71.75: 18 71.75 - 89.68: 6 Dihedral angle restraints: 5435 sinusoidal: 2101 harmonic: 3334 Sorted by residual: dihedral pdb=" CB CYS H 147 " pdb=" SG CYS H 147 " pdb=" SG CYS H 217 " pdb=" CB CYS H 217 " ideal model delta sinusoidal sigma weight residual 93.00 37.82 55.18 1 1.00e+01 1.00e-02 4.12e+01 dihedral pdb=" CA LYS C 78 " pdb=" C LYS C 78 " pdb=" N LEU C 79 " pdb=" CA LEU C 79 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -121.96 35.96 1 1.00e+01 1.00e-02 1.83e+01 ... (remaining 5432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1156 0.063 - 0.126: 226 0.126 - 0.189: 28 0.189 - 0.252: 1 0.252 - 0.315: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA LEU C 286 " pdb=" N LEU C 286 " pdb=" C LEU C 286 " pdb=" CB LEU C 286 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB THR C 47 " pdb=" CA THR C 47 " pdb=" OG1 THR C 47 " pdb=" CG2 THR C 47 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA MET R 279 " pdb=" N MET R 279 " pdb=" C MET R 279 " pdb=" CB MET R 279 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 1409 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 NFI R 401 " -0.068 2.00e-02 2.50e+03 2.32e-01 6.72e+02 pdb=" C11 NFI R 401 " 0.274 2.00e-02 2.50e+03 pdb=" C9 NFI R 401 " 0.161 2.00e-02 2.50e+03 pdb=" N1 NFI R 401 " -0.402 2.00e-02 2.50e+03 pdb=" O2 NFI R 401 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 337 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C ASP B 337 " 0.044 2.00e-02 2.50e+03 pdb=" O ASP B 337 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA B 338 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 201 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C VAL B 201 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL B 201 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY B 202 " 0.014 2.00e-02 2.50e+03 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2093 2.78 - 3.31: 8286 3.31 - 3.84: 14254 3.84 - 4.37: 15785 4.37 - 4.90: 27530 Nonbonded interactions: 67948 Sorted by model distance: nonbonded pdb=" O VAL R 335 " pdb=" OG1 THR R 339 " model vdw 2.255 2.440 nonbonded pdb=" OG SER D 8 " pdb=" OE1 GLN D 11 " model vdw 2.257 2.440 nonbonded pdb=" OG1 THR B 182 " pdb=" OD1 ASN C 119 " model vdw 2.302 2.440 nonbonded pdb=" OG SER C 227 " pdb=" OD1 ASP C 228 " model vdw 2.312 2.440 nonbonded pdb=" NE2 GLN C 220 " pdb=" O LEU C 255 " model vdw 2.322 2.520 ... (remaining 67943 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.290 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: 0.000 Extract box with map and model: 1.750 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.440 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.005 0.105 9165 Z= 0.336 Angle : 0.961 14.541 12411 Z= 0.506 Chirality : 0.051 0.315 1412 Planarity : 0.008 0.232 1570 Dihedral : 15.408 89.683 3279 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 0.62 % Allowed : 20.84 % Favored : 78.54 % 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: -1.79 (0.23), residues: 1130 helix: -0.29 (0.24), residues: 398 sheet: -0.98 (0.33), residues: 256 loop : -2.03 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 169 HIS 0.005 0.001 HIS R 323 PHE 0.020 0.002 PHE H 227 TYR 0.016 0.002 TYR H 223 ARG 0.005 0.001 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 1.035 Fit side-chains REVERT: B 312 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8671 (mmmt) REVERT: H 189 ASP cc_start: 0.7370 (p0) cc_final: 0.7150 (p0) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.2650 time to fit residues: 19.0004 Evaluate side-chains 46 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 312 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS C 132 ASN C 268 ASN C 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9165 Z= 0.212 Angle : 0.521 8.681 12411 Z= 0.268 Chirality : 0.038 0.128 1412 Planarity : 0.003 0.039 1570 Dihedral : 6.006 76.137 1264 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.46 % Allowed : 20.02 % Favored : 77.52 % 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: -0.93 (0.25), residues: 1130 helix: 0.97 (0.26), residues: 403 sheet: -0.86 (0.33), residues: 256 loop : -1.88 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS R 106 PHE 0.011 0.001 PHE B 189 TYR 0.007 0.001 TYR R 287 ARG 0.003 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 43 time to evaluate : 1.200 Fit side-chains REVERT: B 243 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.5390 (mmm) REVERT: H 180 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.5694 (tmm) outliers start: 24 outliers final: 9 residues processed: 64 average time/residue: 0.2114 time to fit residues: 19.7028 Evaluate side-chains 52 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 180 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 110 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9165 Z= 0.166 Angle : 0.488 9.845 12411 Z= 0.250 Chirality : 0.038 0.135 1412 Planarity : 0.003 0.035 1570 Dihedral : 5.714 84.873 1258 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.29 % Allowed : 19.61 % Favored : 77.10 % 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: -0.54 (0.25), residues: 1130 helix: 1.43 (0.27), residues: 402 sheet: -0.82 (0.33), residues: 258 loop : -1.66 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.002 0.000 HIS C 142 PHE 0.010 0.001 PHE B 189 TYR 0.007 0.001 TYR R 49 ARG 0.003 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 43 time to evaluate : 1.105 Fit side-chains REVERT: B 33 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8195 (mm-30) REVERT: B 243 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.5591 (mmm) REVERT: B 266 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7927 (tp) REVERT: C 61 MET cc_start: 0.8109 (ppp) cc_final: 0.7893 (ppp) REVERT: H 180 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.5599 (tmm) outliers start: 32 outliers final: 9 residues processed: 69 average time/residue: 0.2057 time to fit residues: 21.1316 Evaluate side-chains 53 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 180 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 48 optimal weight: 0.0470 chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 0.4980 overall best weight: 3.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9165 Z= 0.213 Angle : 0.487 9.606 12411 Z= 0.250 Chirality : 0.038 0.124 1412 Planarity : 0.003 0.033 1570 Dihedral : 5.449 85.522 1256 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.08 % Allowed : 20.12 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1130 helix: 1.60 (0.27), residues: 402 sheet: -0.78 (0.33), residues: 261 loop : -1.61 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE B 189 TYR 0.006 0.001 TYR R 200 ARG 0.003 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 41 time to evaluate : 1.097 Fit side-chains REVERT: B 33 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8161 (mm-30) REVERT: B 243 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.5681 (mmm) REVERT: B 266 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8100 (tp) REVERT: H 180 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.5638 (tmm) REVERT: H 189 ASP cc_start: 0.7680 (p0) cc_final: 0.7331 (p0) outliers start: 30 outliers final: 14 residues processed: 65 average time/residue: 0.2068 time to fit residues: 19.6759 Evaluate side-chains 56 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 38 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 180 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9165 Z= 0.143 Angle : 0.467 8.998 12411 Z= 0.240 Chirality : 0.038 0.122 1412 Planarity : 0.003 0.034 1570 Dihedral : 5.209 75.981 1256 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.29 % Allowed : 20.23 % Favored : 76.49 % 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: -0.24 (0.26), residues: 1130 helix: 1.71 (0.27), residues: 402 sheet: -0.70 (0.33), residues: 258 loop : -1.51 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.002 0.000 HIS R 106 PHE 0.010 0.001 PHE B 189 TYR 0.009 0.001 TYR R 287 ARG 0.004 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 40 time to evaluate : 1.125 Fit side-chains REVERT: B 24 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.7862 (ptm160) REVERT: B 33 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8201 (mm-30) REVERT: B 243 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.5509 (mmm) REVERT: H 180 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.5744 (tmm) REVERT: H 189 ASP cc_start: 0.7624 (p0) cc_final: 0.7302 (p0) outliers start: 32 outliers final: 16 residues processed: 66 average time/residue: 0.2277 time to fit residues: 21.5251 Evaluate side-chains 58 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 38 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 180 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9165 Z= 0.207 Angle : 0.477 7.538 12411 Z= 0.246 Chirality : 0.038 0.121 1412 Planarity : 0.003 0.033 1570 Dihedral : 5.069 81.184 1254 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.29 % Allowed : 19.92 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1130 helix: 1.73 (0.27), residues: 402 sheet: -0.71 (0.33), residues: 262 loop : -1.49 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE B 189 TYR 0.010 0.001 TYR R 287 ARG 0.003 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 39 time to evaluate : 1.074 Fit side-chains REVERT: B 24 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7972 (ptm160) REVERT: B 33 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8165 (mm-30) REVERT: B 243 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.5645 (mmm) REVERT: H 180 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.5785 (tmm) REVERT: H 189 ASP cc_start: 0.7603 (p0) cc_final: 0.7320 (p0) outliers start: 32 outliers final: 18 residues processed: 65 average time/residue: 0.2254 time to fit residues: 21.1130 Evaluate side-chains 59 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 37 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 180 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9165 Z= 0.265 Angle : 0.497 6.517 12411 Z= 0.256 Chirality : 0.038 0.120 1412 Planarity : 0.003 0.032 1570 Dihedral : 5.146 85.578 1254 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.87 % Allowed : 20.64 % Favored : 76.49 % 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: -0.24 (0.26), residues: 1130 helix: 1.73 (0.27), residues: 402 sheet: -0.80 (0.33), residues: 267 loop : -1.46 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE C 199 TYR 0.010 0.001 TYR R 287 ARG 0.003 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 38 time to evaluate : 1.113 Fit side-chains REVERT: B 24 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7990 (ptm160) REVERT: B 33 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8182 (mm-30) REVERT: B 243 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.5672 (mmm) REVERT: H 180 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.5761 (tmm) REVERT: H 189 ASP cc_start: 0.7622 (p0) cc_final: 0.7355 (p0) outliers start: 28 outliers final: 20 residues processed: 61 average time/residue: 0.2140 time to fit residues: 19.0895 Evaluate side-chains 62 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 38 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 180 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 0.029 9165 Z= 0.207 Angle : 0.477 6.670 12411 Z= 0.246 Chirality : 0.038 0.118 1412 Planarity : 0.003 0.032 1570 Dihedral : 5.142 86.917 1254 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.39 % Allowed : 20.23 % Favored : 76.39 % 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: -0.23 (0.26), residues: 1130 helix: 1.76 (0.27), residues: 402 sheet: -0.79 (0.33), residues: 267 loop : -1.48 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE B 189 TYR 0.008 0.001 TYR R 287 ARG 0.004 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 38 time to evaluate : 1.161 Fit side-chains REVERT: B 24 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7904 (ptm160) REVERT: B 33 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8166 (mm-30) REVERT: B 243 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.5651 (mmm) REVERT: H 180 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.5761 (tmm) REVERT: H 189 ASP cc_start: 0.7568 (p0) cc_final: 0.7306 (p0) outliers start: 33 outliers final: 21 residues processed: 65 average time/residue: 0.2256 time to fit residues: 21.6242 Evaluate side-chains 63 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 38 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 11 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 180 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 60 optimal weight: 0.2980 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 30 optimal weight: 0.0570 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9165 Z= 0.127 Angle : 0.472 8.459 12411 Z= 0.241 Chirality : 0.037 0.122 1412 Planarity : 0.003 0.034 1570 Dihedral : 5.120 87.042 1254 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.98 % Allowed : 20.53 % Favored : 76.49 % 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: -0.15 (0.26), residues: 1130 helix: 1.80 (0.27), residues: 402 sheet: -0.69 (0.33), residues: 262 loop : -1.44 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.002 0.000 HIS R 106 PHE 0.010 0.001 PHE B 189 TYR 0.008 0.001 TYR R 287 ARG 0.004 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 39 time to evaluate : 1.177 Fit side-chains REVERT: B 24 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7800 (ptm160) REVERT: B 33 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8180 (mm-30) REVERT: B 243 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.5453 (mmm) REVERT: H 180 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.5720 (tmm) REVERT: H 189 ASP cc_start: 0.7594 (p0) cc_final: 0.7343 (p0) outliers start: 29 outliers final: 19 residues processed: 63 average time/residue: 0.2258 time to fit residues: 20.4321 Evaluate side-chains 59 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 36 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 11 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 180 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 0.0470 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 94 optimal weight: 10.0000 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9165 Z= 0.115 Angle : 0.485 9.137 12411 Z= 0.244 Chirality : 0.037 0.127 1412 Planarity : 0.003 0.034 1570 Dihedral : 5.095 86.563 1254 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.36 % Allowed : 21.25 % Favored : 76.39 % 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: -0.12 (0.26), residues: 1130 helix: 1.85 (0.27), residues: 402 sheet: -0.69 (0.33), residues: 267 loop : -1.45 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.004 0.000 HIS R 106 PHE 0.010 0.001 PHE B 189 TYR 0.007 0.001 TYR H 50 ARG 0.004 0.000 ARG R 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 40 time to evaluate : 1.171 Fit side-chains REVERT: B 24 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7819 (ptm160) REVERT: B 243 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.5331 (mmm) REVERT: H 180 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.5731 (tmm) REVERT: H 189 ASP cc_start: 0.7579 (p0) cc_final: 0.7303 (p0) outliers start: 23 outliers final: 18 residues processed: 59 average time/residue: 0.2388 time to fit residues: 20.3460 Evaluate side-chains 61 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 40 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 11 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 180 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 30.0000 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.032990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2090 r_free = 0.2090 target = 0.026686 restraints weight = 82058.174| |-----------------------------------------------------------------------------| r_work (start): 0.2074 rms_B_bonded: 3.29 r_work: 0.1994 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.1994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9181 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9165 Z= 0.129 Angle : 0.479 9.158 12411 Z= 0.242 Chirality : 0.037 0.125 1412 Planarity : 0.003 0.033 1570 Dihedral : 5.086 85.899 1254 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.26 % Allowed : 21.46 % Favored : 76.28 % 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: -0.08 (0.26), residues: 1130 helix: 1.89 (0.27), residues: 402 sheet: -0.68 (0.33), residues: 267 loop : -1.43 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.004 0.001 HIS R 106 PHE 0.009 0.001 PHE B 189 TYR 0.006 0.001 TYR R 287 ARG 0.004 0.000 ARG R 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1784.09 seconds wall clock time: 33 minutes 42.98 seconds (2022.98 seconds total)