Starting phenix.real_space_refine on Wed Feb 14 11:20:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9a_33069/02_2024/7x9a_33069_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9a_33069/02_2024/7x9a_33069.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9a_33069/02_2024/7x9a_33069_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9a_33069/02_2024/7x9a_33069_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9a_33069/02_2024/7x9a_33069_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9a_33069/02_2024/7x9a_33069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9a_33069/02_2024/7x9a_33069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9a_33069/02_2024/7x9a_33069_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9a_33069/02_2024/7x9a_33069_updated.pdb" } resolution = 3.2 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= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2000 atoms to isotropic. 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 4591 2.51 5 N 1210 2.21 5 O 1301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 146": "NH1" <-> "NH2" Residue "R GLU 257": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "P ARG 25": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7156 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2427 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1623 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2443 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 384 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "P" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 31} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 4.28, per 1000 atoms: 0.60 Number of scatterers: 7156 At special positions: 0 Unit cell: (114.95, 124.355, 85.69, 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 1301 8.00 N 1210 7.00 C 4591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 33 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS R 113 " - pdb=" SG CYS R 198 " 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: 2.81 Conformation dependent library (CDL) restraints added in 1.3 seconds 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 9 sheets defined 39.1% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'R' and resid 38 through 66 Processing helix chain 'R' and resid 74 through 103 removed outlier: 5.332A pdb=" N LEU R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) Proline residue: R 95 - end of helix removed outlier: 3.675A pdb=" N LEU R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 142 Proline residue: R 117 - end of helix Processing helix chain 'R' and resid 152 through 175 Proline residue: R 172 - end of helix Processing helix chain 'R' and resid 205 through 219 Processing helix chain 'R' and resid 222 through 246 removed outlier: 3.694A pdb=" N ILE R 234 " --> pdb=" O CYS R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 286 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 298 through 319 removed outlier: 4.141A pdb=" N LEU R 303 " --> pdb=" O ASN R 299 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA R 309 " --> pdb=" O CYS R 305 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS R 314 " --> pdb=" O MET R 310 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN R 316 " --> pdb=" O SER R 312 " (cutoff:3.500A) Proline residue: R 317 - end of helix Processing helix chain 'R' and resid 325 through 328 No H-bonds generated for 'chain 'R' and resid 325 through 328' Processing helix chain 'A' and resid 10 through 32 Processing helix chain 'A' and resid 46 through 49 No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.798A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 10 through 13 Processing helix chain 'B' and resid 15 through 24 removed outlier: 3.602A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.130A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 removed outlier: 4.033A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'P' and resid 14 through 31 Processing sheet with id= A, first strand: chain 'R' and resid 178 through 180 Processing sheet with id= B, first strand: chain 'A' and resid 320 through 324 removed outlier: 3.692A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.809A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.027A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.507A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.705A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.754A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 276 through 278 Processing sheet with id= I, first strand: chain 'B' and resid 336 through 339 330 hydrogen bonds defined for protein. 960 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: 1.79 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2312 1.34 - 1.46: 1772 1.46 - 1.58: 3151 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 7310 Sorted by residual: bond pdb=" CB TYC P 36 " pdb=" CG TYC P 36 " ideal model delta sigma weight residual 1.528 1.391 0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C TYC P 36 " pdb=" NXT TYC P 36 " ideal model delta sigma weight residual 1.451 1.330 0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" N TRP R 288 " pdb=" CA TRP R 288 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.25e+00 bond pdb=" C TYC P 36 " pdb=" O TYC P 36 " ideal model delta sigma weight residual 1.185 1.229 -0.044 2.00e-02 2.50e+03 4.95e+00 bond pdb=" CZ TYC P 36 " pdb=" OH TYC P 36 " ideal model delta sigma weight residual 1.401 1.359 0.042 2.00e-02 2.50e+03 4.35e+00 ... (remaining 7305 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.32: 201 107.32 - 114.01: 4198 114.01 - 120.71: 3052 120.71 - 127.41: 2445 127.41 - 134.10: 70 Bond angle restraints: 9966 Sorted by residual: angle pdb=" CE1 TYC P 36 " pdb=" CZ TYC P 36 " pdb=" OH TYC P 36 " ideal model delta sigma weight residual 110.51 120.03 -9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CE2 TYC P 36 " pdb=" CZ TYC P 36 " pdb=" OH TYC P 36 " ideal model delta sigma weight residual 129.45 120.00 9.45 3.00e+00 1.11e-01 9.92e+00 angle pdb=" CA LEU R 94 " pdb=" CB LEU R 94 " pdb=" CG LEU R 94 " ideal model delta sigma weight residual 116.30 125.65 -9.35 3.50e+00 8.16e-02 7.14e+00 angle pdb=" C TRP R 288 " pdb=" N ASN R 289 " pdb=" CA ASN R 289 " ideal model delta sigma weight residual 121.54 126.18 -4.64 1.91e+00 2.74e-01 5.89e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 121.54 126.15 -4.61 1.91e+00 2.74e-01 5.83e+00 ... (remaining 9961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 3991 15.37 - 30.74: 231 30.74 - 46.11: 58 46.11 - 61.48: 5 61.48 - 76.85: 2 Dihedral angle restraints: 4287 sinusoidal: 1503 harmonic: 2784 Sorted by residual: dihedral pdb=" CB CYS R 33 " pdb=" SG CYS R 33 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual -86.00 -116.46 30.46 1 1.00e+01 1.00e-02 1.32e+01 dihedral pdb=" CA ASP R 86 " pdb=" CB ASP R 86 " pdb=" CG ASP R 86 " pdb=" OD1 ASP R 86 " ideal model delta sinusoidal sigma weight residual -30.00 -85.72 55.72 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASP R 31 " pdb=" CB ASP R 31 " pdb=" CG ASP R 31 " pdb=" OD1 ASP R 31 " ideal model delta sinusoidal sigma weight residual -30.00 -80.64 50.64 1 2.00e+01 2.50e-03 8.78e+00 ... (remaining 4284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 764 0.033 - 0.066: 309 0.066 - 0.099: 79 0.099 - 0.131: 24 0.131 - 0.164: 2 Chirality restraints: 1178 Sorted by residual: chirality pdb=" CA TRP R 288 " pdb=" N TRP R 288 " pdb=" C TRP R 288 " pdb=" CB TRP R 288 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA LEU R 94 " pdb=" N LEU R 94 " pdb=" C LEU R 94 " pdb=" CB LEU R 94 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1175 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 288 " -0.012 2.00e-02 2.50e+03 8.43e-03 1.77e+00 pdb=" CG TRP R 288 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP R 288 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP R 288 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 288 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP R 288 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 288 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 288 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 288 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 288 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 171 " -0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO R 172 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO R 172 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 172 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 222 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.48e+00 pdb=" N PRO R 223 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO R 223 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 223 " -0.017 5.00e-02 4.00e+02 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1639 2.78 - 3.31: 7057 3.31 - 3.84: 12091 3.84 - 4.37: 13654 4.37 - 4.90: 23517 Nonbonded interactions: 57958 Sorted by model distance: nonbonded pdb=" O TRP R 276 " pdb=" OG1 THR R 280 " model vdw 2.251 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.257 2.440 nonbonded pdb=" O LEU B 210 " pdb=" N ARG B 219 " model vdw 2.284 2.520 nonbonded pdb=" ND2 ASN B 119 " pdb=" O GLY B 144 " model vdw 2.293 2.520 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.339 2.440 ... (remaining 57953 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 3.840 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.780 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 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 : 0.003 0.137 7310 Z= 0.179 Angle : 0.508 9.515 9966 Z= 0.266 Chirality : 0.039 0.164 1178 Planarity : 0.003 0.031 1262 Dihedral : 10.426 76.846 2471 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: -2.79 (0.25), residues: 935 helix: -0.73 (0.24), residues: 392 sheet: -1.88 (0.36), residues: 172 loop : -3.01 (0.27), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 288 HIS 0.002 0.000 HIS B 142 PHE 0.006 0.001 PHE B 241 TYR 0.013 0.001 TYR R 100 ARG 0.001 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 TYR cc_start: 0.8313 (m-10) cc_final: 0.7955 (m-80) REVERT: B 138 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7730 (mt-10) REVERT: B 264 TYR cc_start: 0.7707 (m-10) cc_final: 0.7270 (m-10) REVERT: B 297 TRP cc_start: 0.7084 (m100) cc_final: 0.6547 (m100) REVERT: C 47 GLU cc_start: 0.7950 (mp0) cc_final: 0.7696 (mp0) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2137 time to fit residues: 61.6753 Evaluate side-chains 149 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 219 GLN R 326 ASN A 244 HIS A 294 ASN A 322 HIS A 347 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 7310 Z= 0.359 Angle : 0.659 9.552 9966 Z= 0.334 Chirality : 0.044 0.192 1178 Planarity : 0.004 0.036 1262 Dihedral : 4.017 26.382 1013 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.44 % Allowed : 16.92 % Favored : 79.64 % 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 (0.27), residues: 935 helix: 0.28 (0.27), residues: 395 sheet: -1.63 (0.37), residues: 161 loop : -2.59 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.009 0.002 HIS B 225 PHE 0.030 0.002 PHE B 199 TYR 0.014 0.002 TYR P 1 ARG 0.004 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8678 (ptm) cc_final: 0.8266 (ptt) REVERT: B 138 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7980 (mt-10) REVERT: B 339 TRP cc_start: 0.8693 (m100) cc_final: 0.8033 (m100) outliers start: 25 outliers final: 18 residues processed: 176 average time/residue: 0.1761 time to fit residues: 42.2974 Evaluate side-chains 166 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 76 ASN R 219 GLN R 326 ASN A 213 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7310 Z= 0.196 Angle : 0.587 10.150 9966 Z= 0.288 Chirality : 0.041 0.181 1178 Planarity : 0.003 0.038 1262 Dihedral : 3.765 30.108 1013 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.89 % Allowed : 18.43 % Favored : 78.68 % 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: -1.27 (0.28), residues: 935 helix: 0.68 (0.28), residues: 400 sheet: -1.59 (0.36), residues: 164 loop : -2.16 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.020 0.001 PHE A 250 TYR 0.015 0.001 TYR A 287 ARG 0.004 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 164 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 TYR cc_start: 0.7498 (m-80) cc_final: 0.7275 (m-80) REVERT: B 339 TRP cc_start: 0.8646 (m100) cc_final: 0.7956 (m100) outliers start: 21 outliers final: 15 residues processed: 172 average time/residue: 0.1695 time to fit residues: 40.1037 Evaluate side-chains 158 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 46 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 0.0060 chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 219 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7310 Z= 0.183 Angle : 0.577 9.721 9966 Z= 0.282 Chirality : 0.041 0.188 1178 Planarity : 0.003 0.039 1262 Dihedral : 3.701 30.199 1013 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.71 % Allowed : 20.50 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.28), residues: 935 helix: 1.02 (0.28), residues: 394 sheet: -1.47 (0.36), residues: 164 loop : -2.02 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.019 0.001 PHE A 274 TYR 0.014 0.001 TYR A 287 ARG 0.005 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 147 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7317 (pmm) cc_final: 0.7053 (pmm) REVERT: A 247 MET cc_start: 0.8617 (ptm) cc_final: 0.8112 (ptt) REVERT: B 57 LYS cc_start: 0.8942 (ptpp) cc_final: 0.8582 (ptpp) REVERT: B 339 TRP cc_start: 0.8610 (m100) cc_final: 0.7953 (m100) REVERT: C 21 MET cc_start: 0.7747 (ppp) cc_final: 0.7544 (tmm) outliers start: 27 outliers final: 20 residues processed: 162 average time/residue: 0.1630 time to fit residues: 36.7526 Evaluate side-chains 158 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 46 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.0370 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 306 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7310 Z= 0.226 Angle : 0.588 9.129 9966 Z= 0.291 Chirality : 0.041 0.196 1178 Planarity : 0.003 0.039 1262 Dihedral : 3.749 27.658 1013 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.13 % Allowed : 20.77 % Favored : 75.10 % 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: -0.85 (0.29), residues: 935 helix: 1.04 (0.28), residues: 399 sheet: -1.50 (0.37), residues: 156 loop : -1.89 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS B 225 PHE 0.021 0.001 PHE B 292 TYR 0.025 0.001 TYR A 287 ARG 0.005 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7314 (pmm) cc_final: 0.7068 (pmm) REVERT: A 247 MET cc_start: 0.8545 (ptm) cc_final: 0.8109 (ptt) REVERT: A 258 TRP cc_start: 0.8763 (m100) cc_final: 0.8520 (m100) REVERT: B 57 LYS cc_start: 0.8889 (ptpp) cc_final: 0.8492 (ptpp) REVERT: B 339 TRP cc_start: 0.8563 (m100) cc_final: 0.7885 (m100) REVERT: C 21 MET cc_start: 0.7772 (ppp) cc_final: 0.7544 (tmm) outliers start: 30 outliers final: 22 residues processed: 174 average time/residue: 0.1774 time to fit residues: 42.4496 Evaluate side-chains 164 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 46 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 85 optimal weight: 0.0470 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 219 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 294 ASN A 306 GLN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7310 Z= 0.203 Angle : 0.611 9.654 9966 Z= 0.297 Chirality : 0.042 0.224 1178 Planarity : 0.003 0.038 1262 Dihedral : 3.803 28.777 1013 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.13 % Allowed : 21.60 % Favored : 74.28 % 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: -0.80 (0.29), residues: 935 helix: 1.05 (0.28), residues: 400 sheet: -1.47 (0.37), residues: 156 loop : -1.84 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.016 0.001 PHE B 199 TYR 0.009 0.001 TYR R 47 ARG 0.006 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8713 (ppp) cc_final: 0.8085 (ppp) REVERT: A 240 MET cc_start: 0.7339 (pmm) cc_final: 0.7099 (pmm) REVERT: A 258 TRP cc_start: 0.8712 (m100) cc_final: 0.8464 (m100) REVERT: B 57 LYS cc_start: 0.8836 (ptpp) cc_final: 0.8548 (ptpp) REVERT: B 339 TRP cc_start: 0.8492 (m100) cc_final: 0.7793 (m100) REVERT: C 21 MET cc_start: 0.7706 (ppp) cc_final: 0.7461 (tmm) outliers start: 30 outliers final: 22 residues processed: 165 average time/residue: 0.1649 time to fit residues: 37.5170 Evaluate side-chains 169 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 219 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7310 Z= 0.227 Angle : 0.625 9.380 9966 Z= 0.305 Chirality : 0.043 0.268 1178 Planarity : 0.003 0.039 1262 Dihedral : 3.788 28.290 1013 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.26 % Allowed : 22.15 % Favored : 73.59 % 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: -0.78 (0.29), residues: 935 helix: 1.06 (0.28), residues: 399 sheet: -1.42 (0.36), residues: 156 loop : -1.83 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.005 0.001 HIS B 225 PHE 0.015 0.001 PHE B 199 TYR 0.024 0.001 TYR A 287 ARG 0.007 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7376 (pmm) cc_final: 0.7162 (pmm) REVERT: B 57 LYS cc_start: 0.8865 (ptpp) cc_final: 0.8513 (ptpp) REVERT: B 264 TYR cc_start: 0.8098 (m-10) cc_final: 0.7282 (m-10) REVERT: B 339 TRP cc_start: 0.8595 (m100) cc_final: 0.7882 (m100) REVERT: C 21 MET cc_start: 0.7779 (ppp) cc_final: 0.7519 (tmm) outliers start: 31 outliers final: 25 residues processed: 162 average time/residue: 0.1687 time to fit residues: 37.8947 Evaluate side-chains 164 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 148 TRP Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 84 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 0.0570 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7310 Z= 0.240 Angle : 0.638 10.225 9966 Z= 0.309 Chirality : 0.043 0.257 1178 Planarity : 0.003 0.038 1262 Dihedral : 3.832 27.556 1013 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.68 % Allowed : 21.32 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.29), residues: 935 helix: 1.06 (0.28), residues: 399 sheet: -1.41 (0.37), residues: 149 loop : -1.76 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.005 0.001 HIS B 225 PHE 0.014 0.001 PHE B 199 TYR 0.017 0.001 TYR A 287 ARG 0.007 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8820 (ppp) cc_final: 0.8114 (ppp) REVERT: A 240 MET cc_start: 0.7478 (pmm) cc_final: 0.7274 (pmm) REVERT: B 57 LYS cc_start: 0.8869 (ptpp) cc_final: 0.8492 (ptpp) REVERT: B 264 TYR cc_start: 0.8138 (m-10) cc_final: 0.7170 (m-10) REVERT: B 292 PHE cc_start: 0.8455 (m-10) cc_final: 0.8180 (m-10) REVERT: B 339 TRP cc_start: 0.8528 (m100) cc_final: 0.7788 (m-10) REVERT: C 21 MET cc_start: 0.7941 (ppp) cc_final: 0.7669 (tmm) outliers start: 34 outliers final: 26 residues processed: 154 average time/residue: 0.1803 time to fit residues: 38.0197 Evaluate side-chains 156 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 148 TRP Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7310 Z= 0.230 Angle : 0.651 10.224 9966 Z= 0.315 Chirality : 0.043 0.255 1178 Planarity : 0.003 0.039 1262 Dihedral : 3.914 27.466 1013 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.13 % Allowed : 22.28 % Favored : 73.59 % 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: -0.74 (0.28), residues: 935 helix: 1.05 (0.28), residues: 400 sheet: -1.34 (0.38), residues: 139 loop : -1.80 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.016 0.001 PHE R 98 TYR 0.015 0.001 TYR A 287 ARG 0.008 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8183 (mmm) cc_final: 0.7903 (tpt) REVERT: B 292 PHE cc_start: 0.8491 (m-10) cc_final: 0.8195 (m-10) REVERT: B 339 TRP cc_start: 0.8535 (m100) cc_final: 0.8263 (m100) REVERT: C 21 MET cc_start: 0.7685 (ppp) cc_final: 0.7387 (tmm) outliers start: 30 outliers final: 26 residues processed: 156 average time/residue: 0.1785 time to fit residues: 38.1514 Evaluate side-chains 159 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 148 TRP Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7310 Z= 0.256 Angle : 0.678 10.186 9966 Z= 0.331 Chirality : 0.043 0.252 1178 Planarity : 0.003 0.039 1262 Dihedral : 4.008 26.632 1013 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.85 % Allowed : 23.52 % Favored : 72.63 % 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: -0.76 (0.28), residues: 935 helix: 1.07 (0.28), residues: 398 sheet: -1.32 (0.39), residues: 132 loop : -1.85 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS B 225 PHE 0.028 0.002 PHE A 274 TYR 0.015 0.001 TYR A 287 ARG 0.009 0.000 ARG R 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8812 (ppp) cc_final: 0.8086 (ppp) REVERT: B 45 MET cc_start: 0.8206 (mmm) cc_final: 0.7933 (tpt) REVERT: B 292 PHE cc_start: 0.8563 (m-10) cc_final: 0.8198 (m-10) REVERT: B 339 TRP cc_start: 0.8541 (m100) cc_final: 0.8264 (m100) REVERT: C 21 MET cc_start: 0.7703 (ppp) cc_final: 0.7416 (tmm) outliers start: 28 outliers final: 24 residues processed: 159 average time/residue: 0.1689 time to fit residues: 36.8289 Evaluate side-chains 161 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 148 TRP Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.096746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077812 restraints weight = 19357.895| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.78 r_work: 0.3158 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7310 Z= 0.252 Angle : 0.705 10.158 9966 Z= 0.347 Chirality : 0.044 0.250 1178 Planarity : 0.003 0.040 1262 Dihedral : 4.043 28.228 1013 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.99 % Allowed : 23.66 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.28), residues: 935 helix: 0.98 (0.28), residues: 403 sheet: -1.36 (0.39), residues: 132 loop : -1.83 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 258 HIS 0.005 0.001 HIS B 225 PHE 0.017 0.001 PHE R 98 TYR 0.014 0.001 TYR A 287 ARG 0.009 0.000 ARG R 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.40 seconds wall clock time: 34 minutes 12.94 seconds (2052.94 seconds total)