Starting phenix.real_space_refine on Wed Feb 14 13:52:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frm_29401/02_2024/8frm_29401_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frm_29401/02_2024/8frm_29401.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frm_29401/02_2024/8frm_29401_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frm_29401/02_2024/8frm_29401_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frm_29401/02_2024/8frm_29401_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frm_29401/02_2024/8frm_29401.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frm_29401/02_2024/8frm_29401.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frm_29401/02_2024/8frm_29401_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frm_29401/02_2024/8frm_29401_updated.pdb" } resolution = 3.14 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= 0.003 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 39 5.16 5 C 5914 2.51 5 N 1546 2.21 5 O 1619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 112": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 207": "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: 9120 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "B" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain: "F" Number of atoms: 2525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2525 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "G" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2712 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 12, 'TRANS': 325} Chain breaks: 2 Chain: "F" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 138 Unusual residues: {'JSG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'JSG:plan-7': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.23, per 1000 atoms: 0.57 Number of scatterers: 9120 At special positions: 0 Unit cell: (82.5, 133.65, 97.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 2 15.00 O 1619 8.00 N 1546 7.00 C 5914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.77 Conformation dependent library (CDL) restraints added in 1.6 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 10 sheets defined 51.7% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 80 through 86 removed outlier: 3.673A pdb=" N LYS A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.816A pdb=" N ILE A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.595A pdb=" N GLN A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 162 removed outlier: 3.728A pdb=" N ALA A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.262A pdb=" N GLY A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.967A pdb=" N ALA A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 80 through 86 Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.837A pdb=" N ILE B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 132 removed outlier: 3.797A pdb=" N GLN B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 148 through 162 removed outlier: 3.940A pdb=" N ALA B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 205 through 210 removed outlier: 4.077A pdb=" N ALA B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'F' and resid 3 through 40 removed outlier: 3.742A pdb=" N GLN F 40 " --> pdb=" O GLY F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 removed outlier: 3.655A pdb=" N ILE F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 3.677A pdb=" N LEU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 95 through 118 removed outlier: 3.617A pdb=" N LEU F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Proline residue: F 104 - end of helix Processing helix chain 'F' and resid 120 through 137 removed outlier: 4.084A pdb=" N VAL F 137 " --> pdb=" O SER F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 143 Processing helix chain 'F' and resid 248 through 250 No H-bonds generated for 'chain 'F' and resid 248 through 250' Processing helix chain 'F' and resid 263 through 274 Processing helix chain 'F' and resid 276 through 286 removed outlier: 3.632A pdb=" N VAL F 280 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE F 281 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET F 285 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 290 No H-bonds generated for 'chain 'F' and resid 288 through 290' Processing helix chain 'F' and resid 302 through 325 removed outlier: 3.542A pdb=" N ARG F 325 " --> pdb=" O THR F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 349 Proline residue: F 334 - end of helix removed outlier: 3.590A pdb=" N TYR F 340 " --> pdb=" O LEU F 337 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY F 341 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA F 345 " --> pdb=" O ILE F 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 41 removed outlier: 4.253A pdb=" N SER G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASN G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 59 through 84 Proline residue: G 68 - end of helix Processing helix chain 'G' and resid 87 through 94 removed outlier: 3.573A pdb=" N VAL G 94 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 122 removed outlier: 3.787A pdb=" N VAL G 111 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 136 removed outlier: 3.827A pdb=" N GLU G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 247 through 260 removed outlier: 3.570A pdb=" N TYR G 260 " --> pdb=" O TYR G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 275 removed outlier: 3.510A pdb=" N ALA G 270 " --> pdb=" O THR G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 293 Processing helix chain 'G' and resid 301 through 327 removed outlier: 3.608A pdb=" N LEU G 327 " --> pdb=" O GLY G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 353 Proline residue: G 340 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 32 through 35 Processing sheet with id= B, first strand: chain 'A' and resid 222 through 227 removed outlier: 6.605A pdb=" N ILE A 217 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU A 226 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA A 215 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 214 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL A 198 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU A 42 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 200 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 17 through 19 removed outlier: 7.791A pdb=" N LYS A 19 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LYS A 28 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 222 through 227 removed outlier: 6.778A pdb=" N ILE B 217 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU B 226 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 215 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS B 214 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL B 198 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU B 42 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE B 200 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 17 through 19 removed outlier: 7.704A pdb=" N LYS B 19 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LYS B 28 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 148 through 152 removed outlier: 4.157A pdb=" N GLU F 148 " --> pdb=" O ALA F 159 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA F 159 " --> pdb=" O GLU F 148 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY F 211 " --> pdb=" O PHE F 228 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 192 through 194 removed outlier: 3.515A pdb=" N VAL F 206 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 149 through 153 Processing sheet with id= I, first strand: chain 'G' and resid 162 through 164 removed outlier: 3.936A pdb=" N GLN G 168 " --> pdb=" O ASN G 164 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN G 191 " --> pdb=" O ASN G 203 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL G 195 " --> pdb=" O GLN G 199 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN G 199 " --> pdb=" O VAL G 195 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 205 through 207 458 hydrogen bonds defined for protein. 1278 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: 3.14 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2119 1.33 - 1.45: 1800 1.45 - 1.57: 5299 1.57 - 1.69: 2 1.69 - 1.81: 72 Bond restraints: 9292 Sorted by residual: bond pdb=" C7 JSG F 401 " pdb=" N2 JSG F 401 " ideal model delta sigma weight residual 1.621 1.320 0.301 2.00e-02 2.50e+03 2.26e+02 bond pdb=" CDO JSG F 401 " pdb=" NAO JSG F 401 " ideal model delta sigma weight residual 1.505 1.325 0.180 2.00e-02 2.50e+03 8.08e+01 bond pdb=" CAN JSG F 401 " pdb=" NAO JSG F 401 " ideal model delta sigma weight residual 1.577 1.448 0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" C1 JSG F 401 " pdb=" O5 JSG F 401 " ideal model delta sigma weight residual 1.533 1.407 0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" CFK JSG F 401 " pdb=" CFL JSG F 401 " ideal model delta sigma weight residual 1.615 1.505 0.110 2.00e-02 2.50e+03 3.01e+01 ... (remaining 9287 not shown) Histogram of bond angle deviations from ideal: 97.54 - 104.84: 129 104.84 - 112.13: 4693 112.13 - 119.43: 3148 119.43 - 126.72: 4461 126.72 - 134.02: 114 Bond angle restraints: 12545 Sorted by residual: angle pdb=" C1 JSG F 401 " pdb=" C2 JSG F 401 " pdb=" N2 JSG F 401 " ideal model delta sigma weight residual 109.69 97.54 12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" CA ARG B 125 " pdb=" C ARG B 125 " pdb=" O ARG B 125 " ideal model delta sigma weight residual 120.82 116.82 4.00 1.05e+00 9.07e-01 1.45e+01 angle pdb=" N ILE F 342 " pdb=" CA ILE F 342 " pdb=" C ILE F 342 " ideal model delta sigma weight residual 111.89 106.44 5.45 1.44e+00 4.82e-01 1.43e+01 angle pdb=" N GLN B 123 " pdb=" CA GLN B 123 " pdb=" C GLN B 123 " ideal model delta sigma weight residual 111.82 107.58 4.24 1.16e+00 7.43e-01 1.34e+01 angle pdb=" CA VAL F 339 " pdb=" C VAL F 339 " pdb=" O VAL F 339 " ideal model delta sigma weight residual 121.05 117.32 3.73 1.11e+00 8.12e-01 1.13e+01 ... (remaining 12540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.42: 5022 18.42 - 36.83: 471 36.83 - 55.25: 70 55.25 - 73.66: 10 73.66 - 92.08: 6 Dihedral angle restraints: 5579 sinusoidal: 2314 harmonic: 3265 Sorted by residual: dihedral pdb=" CGQ JSG F 401 " pdb=" CGN JSG F 401 " pdb=" CGP JSG F 401 " pdb=" OFZ JSG F 401 " ideal model delta sinusoidal sigma weight residual 144.32 52.24 92.08 1 3.00e+01 1.11e-03 1.11e+01 dihedral pdb=" CA MET F 27 " pdb=" C MET F 27 " pdb=" N GLY F 28 " pdb=" CA GLY F 28 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU A 82 " pdb=" CG GLU A 82 " pdb=" CD GLU A 82 " pdb=" OE1 GLU A 82 " ideal model delta sinusoidal sigma weight residual 0.00 -88.81 88.81 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 5576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1117 0.049 - 0.098: 242 0.098 - 0.147: 65 0.147 - 0.197: 3 0.197 - 0.246: 3 Chirality restraints: 1430 Sorted by residual: chirality pdb=" C2 JSG F 401 " pdb=" C1 JSG F 401 " pdb=" C3 JSG F 401 " pdb=" N2 JSG F 401 " both_signs ideal model delta sigma weight residual False -2.57 -2.81 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CAN JSG F 401 " pdb=" CAL JSG F 401 " pdb=" CAP JSG F 401 " pdb=" NAO JSG F 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.76 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1427 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 293 " 0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO F 294 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 294 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 294 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 338 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C ALA F 338 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA F 338 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL F 339 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 122 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C ARG B 122 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG B 122 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN B 123 " -0.010 2.00e-02 2.50e+03 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.11: 2 2.11 - 2.81: 2412 2.81 - 3.51: 12631 3.51 - 4.20: 21670 4.20 - 4.90: 39525 Nonbonded interactions: 76240 Sorted by model distance: nonbonded pdb=" CBE JSG F 401 " pdb=" OBU JSG F 401 " model vdw 1.416 3.470 nonbonded pdb=" CBC JSG F 401 " pdb=" OBS JSG F 401 " model vdw 1.423 3.470 nonbonded pdb=" O GLU G 65 " pdb=" OH TYR G 316 " model vdw 2.229 2.440 nonbonded pdb=" NH1 ARG F 78 " pdb=" OD2 ASP F 82 " model vdw 2.252 2.520 nonbonded pdb=" O ASP A 71 " pdb=" OD1 ASN A 72 " model vdw 2.256 3.040 ... (remaining 76235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 10 through 247) selection = chain 'B' } 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.440 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 28.730 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.301 9292 Z= 0.523 Angle : 0.634 12.146 12545 Z= 0.341 Chirality : 0.045 0.246 1430 Planarity : 0.004 0.051 1563 Dihedral : 14.195 92.078 3479 Min Nonbonded Distance : 1.416 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.46 (0.25), residues: 1111 helix: 0.85 (0.21), residues: 593 sheet: 1.83 (0.54), residues: 110 loop : -0.87 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 123 HIS 0.002 0.001 HIS B 137 PHE 0.016 0.001 PHE F 69 TYR 0.008 0.001 TYR F 6 ARG 0.006 0.000 ARG F 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.062 Fit side-chains REVERT: B 112 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7792 (mt-10) REVERT: B 204 ASN cc_start: 0.8489 (t0) cc_final: 0.8271 (t0) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2665 time to fit residues: 47.0092 Evaluate side-chains 99 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 99 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 HIS F 258 ASN F 296 GLN G 193 GLN ** G 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9292 Z= 0.205 Angle : 0.522 7.466 12545 Z= 0.262 Chirality : 0.042 0.175 1430 Planarity : 0.004 0.050 1563 Dihedral : 8.220 89.620 1336 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.04 % Allowed : 6.67 % Favored : 92.28 % 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: 0.65 (0.25), residues: 1111 helix: 1.11 (0.21), residues: 590 sheet: 1.88 (0.53), residues: 103 loop : -0.89 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 25 HIS 0.002 0.001 HIS B 137 PHE 0.009 0.001 PHE A 173 TYR 0.007 0.001 TYR F 6 ARG 0.006 0.000 ARG F 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.036 Fit side-chains REVERT: B 204 ASN cc_start: 0.8526 (t0) cc_final: 0.8041 (t0) outliers start: 10 outliers final: 8 residues processed: 111 average time/residue: 0.2467 time to fit residues: 36.9252 Evaluate side-chains 106 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 53 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.0060 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 HIS F 296 GLN G 41 ASN ** G 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9292 Z= 0.205 Angle : 0.483 6.163 12545 Z= 0.244 Chirality : 0.041 0.135 1430 Planarity : 0.004 0.050 1563 Dihedral : 7.853 78.242 1336 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.29 % Allowed : 9.07 % Favored : 88.63 % 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: 0.77 (0.25), residues: 1111 helix: 1.24 (0.21), residues: 590 sheet: 1.71 (0.51), residues: 109 loop : -0.89 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 25 HIS 0.002 0.001 HIS G 10 PHE 0.008 0.001 PHE A 173 TYR 0.007 0.001 TYR F 6 ARG 0.006 0.000 ARG F 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 1.067 Fit side-chains REVERT: B 204 ASN cc_start: 0.8576 (t0) cc_final: 0.8037 (t0) outliers start: 22 outliers final: 14 residues processed: 113 average time/residue: 0.2371 time to fit residues: 36.5605 Evaluate side-chains 112 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 290 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN B 81 HIS B 203 HIS F 296 GLN ** G 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9292 Z= 0.361 Angle : 0.558 8.374 12545 Z= 0.279 Chirality : 0.044 0.142 1430 Planarity : 0.004 0.053 1563 Dihedral : 7.872 77.954 1336 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.50 % Allowed : 11.99 % Favored : 85.51 % 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: 0.50 (0.25), residues: 1111 helix: 0.95 (0.21), residues: 596 sheet: 1.25 (0.49), residues: 120 loop : -0.84 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 25 HIS 0.005 0.001 HIS B 137 PHE 0.013 0.001 PHE A 173 TYR 0.010 0.001 TYR F 6 ARG 0.010 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.983 Fit side-chains REVERT: B 204 ASN cc_start: 0.8675 (t0) cc_final: 0.8098 (t0) outliers start: 24 outliers final: 18 residues processed: 118 average time/residue: 0.2415 time to fit residues: 39.1529 Evaluate side-chains 119 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 290 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 0.0370 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 0.0070 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 HIS F 10 GLN F 296 GLN ** G 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9292 Z= 0.167 Angle : 0.474 6.710 12545 Z= 0.240 Chirality : 0.040 0.137 1430 Planarity : 0.003 0.052 1563 Dihedral : 7.627 79.070 1336 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.77 % Allowed : 13.24 % Favored : 84.98 % 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 (0.25), residues: 1111 helix: 1.26 (0.21), residues: 595 sheet: 1.21 (0.49), residues: 120 loop : -0.88 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 25 HIS 0.001 0.000 HIS A 81 PHE 0.007 0.001 PHE B 32 TYR 0.007 0.001 TYR F 6 ARG 0.006 0.000 ARG F 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 1.048 Fit side-chains REVERT: B 204 ASN cc_start: 0.8615 (t0) cc_final: 0.8104 (t0) REVERT: F 145 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7641 (mtm-85) REVERT: G 56 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7598 (mp) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 0.2361 time to fit residues: 36.7809 Evaluate side-chains 114 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 263 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 HIS F 10 GLN F 296 GLN ** G 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9292 Z= 0.287 Angle : 0.509 6.263 12545 Z= 0.257 Chirality : 0.042 0.139 1430 Planarity : 0.004 0.053 1563 Dihedral : 7.648 79.785 1336 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.29 % Allowed : 14.08 % Favored : 83.63 % 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: 0.60 (0.25), residues: 1111 helix: 1.08 (0.21), residues: 602 sheet: 1.21 (0.50), residues: 119 loop : -0.88 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 25 HIS 0.003 0.001 HIS B 137 PHE 0.011 0.001 PHE A 173 TYR 0.008 0.001 TYR F 6 ARG 0.006 0.000 ARG F 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 0.972 Fit side-chains REVERT: B 204 ASN cc_start: 0.8679 (t0) cc_final: 0.8089 (t0) REVERT: F 82 ASP cc_start: 0.8339 (p0) cc_final: 0.7928 (p0) REVERT: G 56 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7611 (mp) outliers start: 22 outliers final: 17 residues processed: 118 average time/residue: 0.2221 time to fit residues: 36.0585 Evaluate side-chains 119 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 290 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 HIS F 10 GLN F 296 GLN ** G 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 9292 Z= 0.539 Angle : 0.643 9.054 12545 Z= 0.322 Chirality : 0.048 0.175 1430 Planarity : 0.005 0.055 1563 Dihedral : 8.164 80.329 1336 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.82 % Allowed : 13.87 % Favored : 83.32 % 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: -0.02 (0.25), residues: 1111 helix: 0.52 (0.21), residues: 595 sheet: 0.96 (0.50), residues: 119 loop : -1.03 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 25 HIS 0.007 0.001 HIS B 137 PHE 0.017 0.002 PHE A 173 TYR 0.011 0.002 TYR F 6 ARG 0.004 0.001 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 1.036 Fit side-chains REVERT: B 25 TRP cc_start: 0.8086 (m100) cc_final: 0.7841 (m100) REVERT: G 56 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7647 (mp) outliers start: 27 outliers final: 18 residues processed: 119 average time/residue: 0.2362 time to fit residues: 38.9938 Evaluate side-chains 116 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 290 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 96 optimal weight: 20.0000 chunk 101 optimal weight: 0.0670 chunk 92 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 10 GLN F 296 GLN G 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9292 Z= 0.183 Angle : 0.488 7.373 12545 Z= 0.250 Chirality : 0.040 0.146 1430 Planarity : 0.004 0.055 1563 Dihedral : 7.840 82.471 1336 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.88 % Allowed : 15.22 % Favored : 82.90 % 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: 0.42 (0.25), residues: 1111 helix: 0.95 (0.21), residues: 602 sheet: 0.97 (0.50), residues: 119 loop : -0.94 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 25 HIS 0.003 0.001 HIS B 203 PHE 0.009 0.001 PHE G 226 TYR 0.009 0.001 TYR F 6 ARG 0.004 0.000 ARG F 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.953 Fit side-chains REVERT: B 204 ASN cc_start: 0.8673 (t0) cc_final: 0.8061 (t0) REVERT: G 56 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7669 (mp) outliers start: 18 outliers final: 12 residues processed: 112 average time/residue: 0.2392 time to fit residues: 36.7283 Evaluate side-chains 110 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 290 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 0.0040 chunk 59 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 104 optimal weight: 0.0170 chunk 63 optimal weight: 9.9990 overall best weight: 0.4632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9292 Z= 0.173 Angle : 0.475 7.206 12545 Z= 0.243 Chirality : 0.040 0.137 1430 Planarity : 0.004 0.054 1563 Dihedral : 7.536 83.650 1336 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.36 % Allowed : 15.64 % Favored : 83.00 % 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: 0.68 (0.25), residues: 1111 helix: 1.22 (0.21), residues: 602 sheet: 0.90 (0.50), residues: 121 loop : -0.87 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 25 HIS 0.003 0.001 HIS B 203 PHE 0.009 0.001 PHE G 226 TYR 0.006 0.001 TYR F 6 ARG 0.004 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 1.094 Fit side-chains REVERT: A 214 HIS cc_start: 0.8565 (t-90) cc_final: 0.8129 (t-90) REVERT: B 204 ASN cc_start: 0.8665 (t0) cc_final: 0.8129 (t0) REVERT: G 56 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7608 (mp) outliers start: 13 outliers final: 9 residues processed: 107 average time/residue: 0.2443 time to fit residues: 35.7258 Evaluate side-chains 108 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 263 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.0070 chunk 26 optimal weight: 2.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 ASN ** G 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9292 Z= 0.206 Angle : 0.488 7.595 12545 Z= 0.247 Chirality : 0.041 0.140 1430 Planarity : 0.004 0.054 1563 Dihedral : 7.447 83.861 1336 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.15 % Allowed : 16.06 % Favored : 82.79 % 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: 0.68 (0.25), residues: 1111 helix: 1.24 (0.21), residues: 600 sheet: 0.87 (0.50), residues: 121 loop : -0.88 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 25 HIS 0.002 0.000 HIS B 137 PHE 0.009 0.001 PHE G 226 TYR 0.007 0.001 TYR F 6 ARG 0.004 0.000 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.007 Fit side-chains REVERT: A 214 HIS cc_start: 0.8570 (t-90) cc_final: 0.8142 (t-90) REVERT: B 204 ASN cc_start: 0.8652 (t0) cc_final: 0.8128 (t0) REVERT: G 56 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7652 (mp) outliers start: 11 outliers final: 9 residues processed: 106 average time/residue: 0.2295 time to fit residues: 33.9479 Evaluate side-chains 109 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.0020 chunk 89 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 overall best weight: 0.5126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 ASN ** G 207 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 = 0.3559 r_free = 0.3559 target = 0.146831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.103153 restraints weight = 9834.092| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.54 r_work: 0.2920 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 9292 Z= 0.251 Angle : 0.840 59.192 12545 Z= 0.490 Chirality : 0.043 0.517 1430 Planarity : 0.004 0.058 1563 Dihedral : 7.508 83.861 1336 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.15 % Allowed : 16.06 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1111 helix: 1.25 (0.21), residues: 600 sheet: 0.87 (0.50), residues: 121 loop : -0.88 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 25 HIS 0.002 0.000 HIS B 137 PHE 0.008 0.001 PHE G 226 TYR 0.007 0.001 TYR F 6 ARG 0.004 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2063.95 seconds wall clock time: 38 minutes 15.69 seconds (2295.69 seconds total)