Starting phenix.real_space_refine on Wed Sep 25 03:29:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9u_31827/09_2024/7v9u_31827.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9u_31827/09_2024/7v9u_31827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9u_31827/09_2024/7v9u_31827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9u_31827/09_2024/7v9u_31827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9u_31827/09_2024/7v9u_31827.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9u_31827/09_2024/7v9u_31827.cif" } resolution = 3.12 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= 0.060 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 209 5.49 5 S 18 5.16 5 C 5183 2.51 5 N 1687 2.21 5 O 2257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9354 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2478 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain: "B" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2478 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain: "D" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "E" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1205 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 8, 'rna3p_pur': 22, 'rna3p_pyr': 24} Link IDs: {'rna2p': 11, 'rna3p': 45} Chain breaks: 1 Chain: "F" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "G" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 10, 'rna3p_pur': 21, 'rna3p_pyr': 23} Link IDs: {'rna2p': 14, 'rna3p': 43} Chain breaks: 1 Chain: "H" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Time building chain proxies: 6.43, per 1000 atoms: 0.69 Number of scatterers: 9354 At special positions: 0 Unit cell: (123.25, 153, 93.5, 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 18 16.00 P 209 15.00 O 2257 8.00 N 1687 7.00 C 5183 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 - 3.00 Amino acid : True - 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: 2.24 Conformation dependent library (CDL) restraints added in 627.3 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 58.6% alpha, 9.4% beta 65 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 removed outlier: 3.725A pdb=" N ASN A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 33 through 42 removed outlier: 3.674A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.645A pdb=" N PHE A 46 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.521A pdb=" N ALA A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 removed outlier: 3.905A pdb=" N LEU A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.728A pdb=" N PHE A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.662A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.644A pdb=" N ASP A 178 " --> pdb=" O CYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 224 removed outlier: 3.588A pdb=" N VAL A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 3.998A pdb=" N GLY A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 272 removed outlier: 3.813A pdb=" N ILE A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.732A pdb=" N ILE A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 310 removed outlier: 3.812A pdb=" N HIS A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 16 removed outlier: 3.706A pdb=" N LEU B 15 " --> pdb=" O ARG B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 33 through 42 Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.544A pdb=" N PHE B 46 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 84 removed outlier: 3.576A pdb=" N ALA B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.508A pdb=" N ALA B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.735A pdb=" N PHE B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.653A pdb=" N LEU B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.633A pdb=" N ASP B 178 " --> pdb=" O CYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.644A pdb=" N VAL B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 257 through 272 removed outlier: 4.795A pdb=" N ILE B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 removed outlier: 4.146A pdb=" N HIS B 280 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 277 through 281' Processing helix chain 'B' and resid 284 through 292 removed outlier: 4.025A pdb=" N ILE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 310 removed outlier: 3.641A pdb=" N HIS B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 53 removed outlier: 3.784A pdb=" N ARG A 63 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 195 Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 121 removed outlier: 4.733A pdb=" N VAL A 226 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.951A pdb=" N ARG B 61 " --> pdb=" O LYS B 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 195 removed outlier: 3.575A pdb=" N PHE B 114 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 121 removed outlier: 4.761A pdb=" N VAL B 226 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 243 226 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 163 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 2.58 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: 1851 1.33 - 1.45: 3295 1.45 - 1.57: 4394 1.57 - 1.69: 408 1.69 - 1.81: 26 Bond restraints: 9974 Sorted by residual: bond pdb=" C3' DG C 73 " pdb=" O3' DG C 73 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" C3' DG D 73 " pdb=" O3' DG D 73 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" C4' DC C 83 " pdb=" C3' DC C 83 " ideal model delta sigma weight residual 1.523 1.500 0.023 2.00e-02 2.50e+03 1.30e+00 bond pdb=" CG1 ILE B 145 " pdb=" CD1 ILE B 145 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.21e+00 bond pdb=" C3' A G 66 " pdb=" O3' A G 66 " ideal model delta sigma weight residual 1.417 1.432 -0.015 1.50e-02 4.44e+03 1.06e+00 ... (remaining 9969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 13932 1.51 - 3.01: 391 3.01 - 4.52: 71 4.52 - 6.02: 18 6.02 - 7.53: 4 Bond angle restraints: 14416 Sorted by residual: angle pdb=" N ILE B 278 " pdb=" CA ILE B 278 " pdb=" C ILE B 278 " ideal model delta sigma weight residual 111.91 108.84 3.07 8.90e-01 1.26e+00 1.19e+01 angle pdb=" N TYR B 260 " pdb=" CA TYR B 260 " pdb=" C TYR B 260 " ideal model delta sigma weight residual 113.43 109.51 3.92 1.26e+00 6.30e-01 9.68e+00 angle pdb=" C3' A G 66 " pdb=" O3' A G 66 " pdb=" P U G 67 " ideal model delta sigma weight residual 120.20 124.27 -4.07 1.50e+00 4.44e-01 7.35e+00 angle pdb=" C ALA B 196 " pdb=" CA ALA B 196 " pdb=" CB ALA B 196 " ideal model delta sigma weight residual 110.42 115.76 -5.34 1.99e+00 2.53e-01 7.20e+00 angle pdb=" C2' C G 65 " pdb=" C1' C G 65 " pdb=" N1 C G 65 " ideal model delta sigma weight residual 112.00 116.00 -4.00 1.50e+00 4.44e-01 7.10e+00 ... (remaining 14411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 5363 35.98 - 71.96: 622 71.96 - 107.93: 46 107.93 - 143.91: 8 143.91 - 179.89: 13 Dihedral angle restraints: 6052 sinusoidal: 4248 harmonic: 1804 Sorted by residual: dihedral pdb=" O4' U E 52 " pdb=" C1' U E 52 " pdb=" N1 U E 52 " pdb=" C2 U E 52 " ideal model delta sinusoidal sigma weight residual 200.00 47.39 152.61 1 1.50e+01 4.44e-03 8.06e+01 dihedral pdb=" O4' C E 15 " pdb=" C1' C E 15 " pdb=" N1 C E 15 " pdb=" C2 C E 15 " ideal model delta sinusoidal sigma weight residual 200.00 48.83 151.17 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" O4' U E 68 " pdb=" C1' U E 68 " pdb=" N1 U E 68 " pdb=" C2 U E 68 " ideal model delta sinusoidal sigma weight residual -160.00 -30.80 -129.20 1 1.50e+01 4.44e-03 6.96e+01 ... (remaining 6049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1338 0.039 - 0.079: 305 0.079 - 0.118: 69 0.118 - 0.157: 15 0.157 - 0.197: 4 Chirality restraints: 1731 Sorted by residual: chirality pdb=" C3' A E 66 " pdb=" C4' A E 66 " pdb=" O3' A E 66 " pdb=" C2' A E 66 " both_signs ideal model delta sigma weight residual False -2.48 -2.28 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" C3' A G 66 " pdb=" C4' A G 66 " pdb=" O3' A G 66 " pdb=" C2' A G 66 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" C1' C E 65 " pdb=" O4' C E 65 " pdb=" C2' C E 65 " pdb=" N1 C E 65 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 1728 not shown) Planarity restraints: 1057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 236 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO A 237 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 220 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO B 221 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 221 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 221 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A E 13 " 0.021 2.00e-02 2.50e+03 9.76e-03 2.62e+00 pdb=" N9 A E 13 " -0.022 2.00e-02 2.50e+03 pdb=" C8 A E 13 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A E 13 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A E 13 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A E 13 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A E 13 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A E 13 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A E 13 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A E 13 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A E 13 " -0.002 2.00e-02 2.50e+03 ... (remaining 1054 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 737 2.72 - 3.27: 8464 3.27 - 3.81: 16545 3.81 - 4.36: 20877 4.36 - 4.90: 31372 Nonbonded interactions: 77995 Sorted by model distance: nonbonded pdb=" O THR A 301 " pdb=" OG SER A 304 " model vdw 2.180 3.040 nonbonded pdb=" O ASN B 142 " pdb=" OG SER B 146 " model vdw 2.187 3.040 nonbonded pdb=" O THR B 301 " pdb=" OG SER B 304 " model vdw 2.187 3.040 nonbonded pdb=" OD2 ASP A 292 " pdb=" OG SER A 295 " model vdw 2.191 3.040 nonbonded pdb=" O SER A 218 " pdb=" O2' G F 1 " model vdw 2.197 3.040 ... (remaining 77990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'G' and resid 9 through 81) } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.090 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.004 0.043 9974 Z= 0.252 Angle : 0.633 7.531 14416 Z= 0.336 Chirality : 0.037 0.197 1731 Planarity : 0.005 0.053 1057 Dihedral : 25.349 179.890 4892 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -1.53 (0.32), residues: 614 helix: -0.90 (0.29), residues: 308 sheet: 0.62 (0.69), residues: 62 loop : -1.46 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 284 HIS 0.009 0.001 HIS B 269 PHE 0.025 0.002 PHE B 92 TYR 0.011 0.001 TYR A 179 ARG 0.007 0.001 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.6634 (pttp) cc_final: 0.6325 (mtmm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3282 time to fit residues: 26.2223 Evaluate side-chains 50 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 10.0000 chunk 57 optimal weight: 0.0670 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9974 Z= 0.197 Angle : 0.596 6.881 14416 Z= 0.312 Chirality : 0.037 0.233 1731 Planarity : 0.005 0.049 1057 Dihedral : 27.266 179.954 3650 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.36 % Allowed : 8.70 % Favored : 90.94 % 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: -1.05 (0.32), residues: 614 helix: -0.36 (0.29), residues: 312 sheet: 0.76 (0.69), residues: 62 loop : -1.44 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 78 HIS 0.006 0.001 HIS B 269 PHE 0.016 0.002 PHE B 92 TYR 0.015 0.001 TYR A 302 ARG 0.005 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.690 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.2999 time to fit residues: 23.2185 Evaluate side-chains 49 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 202 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9974 Z= 0.235 Angle : 0.604 6.791 14416 Z= 0.316 Chirality : 0.037 0.229 1731 Planarity : 0.005 0.050 1057 Dihedral : 27.175 179.892 3650 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.72 % Allowed : 11.78 % Favored : 87.50 % 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: -1.08 (0.32), residues: 614 helix: -0.27 (0.29), residues: 310 sheet: 0.62 (0.69), residues: 62 loop : -1.58 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 284 HIS 0.006 0.001 HIS A 269 PHE 0.015 0.002 PHE B 92 TYR 0.017 0.002 TYR A 302 ARG 0.007 0.001 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.793 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 58 average time/residue: 0.2866 time to fit residues: 21.9456 Evaluate side-chains 52 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 202 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9974 Z= 0.244 Angle : 0.609 7.238 14416 Z= 0.318 Chirality : 0.037 0.232 1731 Planarity : 0.005 0.051 1057 Dihedral : 27.131 179.929 3650 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.27 % Allowed : 15.22 % Favored : 83.51 % 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: -1.12 (0.32), residues: 614 helix: -0.29 (0.29), residues: 310 sheet: 0.59 (0.69), residues: 62 loop : -1.62 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 78 HIS 0.007 0.001 HIS B 269 PHE 0.013 0.002 PHE B 92 TYR 0.013 0.002 TYR A 302 ARG 0.009 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.670 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.2927 time to fit residues: 22.0738 Evaluate side-chains 53 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 202 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.0010 chunk 62 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9974 Z= 0.182 Angle : 0.587 6.847 14416 Z= 0.307 Chirality : 0.036 0.233 1731 Planarity : 0.005 0.060 1057 Dihedral : 27.124 179.583 3650 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.09 % Allowed : 15.94 % Favored : 82.97 % 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: -0.95 (0.33), residues: 614 helix: -0.19 (0.29), residues: 314 sheet: 0.66 (0.69), residues: 62 loop : -1.50 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 78 HIS 0.006 0.001 HIS B 269 PHE 0.011 0.001 PHE B 92 TYR 0.012 0.001 TYR A 302 ARG 0.007 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.688 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 0.2950 time to fit residues: 21.3862 Evaluate side-chains 55 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 202 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9974 Z= 0.249 Angle : 0.617 7.499 14416 Z= 0.321 Chirality : 0.038 0.232 1731 Planarity : 0.005 0.050 1057 Dihedral : 27.092 179.883 3650 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.54 % Allowed : 16.85 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.32), residues: 614 helix: -0.28 (0.29), residues: 314 sheet: 0.61 (0.69), residues: 62 loop : -1.58 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 78 HIS 0.007 0.001 HIS B 269 PHE 0.012 0.002 PHE B 92 TYR 0.016 0.002 TYR A 302 ARG 0.005 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 64 average time/residue: 0.2952 time to fit residues: 24.8891 Evaluate side-chains 61 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 0.2980 chunk 61 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9974 Z= 0.173 Angle : 0.591 7.977 14416 Z= 0.308 Chirality : 0.036 0.234 1731 Planarity : 0.004 0.046 1057 Dihedral : 27.087 179.528 3650 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.99 % Allowed : 17.57 % Favored : 80.43 % 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: -0.84 (0.33), residues: 614 helix: -0.10 (0.29), residues: 314 sheet: 0.74 (0.69), residues: 62 loop : -1.43 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 78 HIS 0.006 0.001 HIS B 269 PHE 0.010 0.001 PHE B 92 TYR 0.009 0.001 TYR A 302 ARG 0.004 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 59 average time/residue: 0.2600 time to fit residues: 20.8014 Evaluate side-chains 61 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9974 Z= 0.271 Angle : 0.626 7.750 14416 Z= 0.327 Chirality : 0.038 0.232 1731 Planarity : 0.005 0.050 1057 Dihedral : 27.080 179.861 3650 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.54 % Allowed : 17.03 % Favored : 80.43 % 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: -1.06 (0.33), residues: 614 helix: -0.22 (0.29), residues: 310 sheet: 0.56 (0.69), residues: 62 loop : -1.60 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 284 HIS 0.007 0.001 HIS B 269 PHE 0.013 0.002 PHE B 215 TYR 0.011 0.002 TYR A 179 ARG 0.007 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 13 residues processed: 60 average time/residue: 0.2745 time to fit residues: 22.3293 Evaluate side-chains 61 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9974 Z= 0.357 Angle : 0.685 7.809 14416 Z= 0.356 Chirality : 0.041 0.233 1731 Planarity : 0.005 0.053 1057 Dihedral : 27.151 179.367 3650 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.90 % Allowed : 16.67 % Favored : 80.43 % 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: -1.40 (0.32), residues: 614 helix: -0.53 (0.28), residues: 310 sheet: 0.41 (0.69), residues: 62 loop : -1.73 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP B 284 HIS 0.008 0.001 HIS B 269 PHE 0.016 0.002 PHE B 215 TYR 0.014 0.002 TYR A 179 ARG 0.006 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 15 residues processed: 59 average time/residue: 0.2572 time to fit residues: 20.5216 Evaluate side-chains 62 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 18 optimal weight: 0.0870 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9974 Z= 0.162 Angle : 0.578 7.291 14416 Z= 0.301 Chirality : 0.036 0.234 1731 Planarity : 0.004 0.046 1057 Dihedral : 27.071 179.763 3650 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.45 % Allowed : 17.93 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.33), residues: 614 helix: -0.12 (0.29), residues: 316 sheet: 0.70 (0.70), residues: 62 loop : -1.42 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 78 HIS 0.006 0.001 HIS A 269 PHE 0.010 0.001 PHE B 92 TYR 0.007 0.001 TYR B 260 ARG 0.004 0.000 ARG B 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 58 average time/residue: 0.2705 time to fit residues: 21.1669 Evaluate side-chains 56 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.188198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.145293 restraints weight = 14892.705| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.45 r_work: 0.3721 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.003 0.037 9974 Z= 0.175 Angle : 0.574 8.433 14416 Z= 0.300 Chirality : 0.036 0.234 1731 Planarity : 0.004 0.047 1057 Dihedral : 27.040 179.719 3650 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.99 % Allowed : 17.21 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.33), residues: 614 helix: -0.01 (0.30), residues: 316 sheet: 0.76 (0.70), residues: 62 loop : -1.36 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 78 HIS 0.006 0.001 HIS B 269 PHE 0.009 0.001 PHE B 92 TYR 0.020 0.001 TYR B 260 ARG 0.005 0.000 ARG A 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1848.58 seconds wall clock time: 37 minutes 53.98 seconds (2273.98 seconds total)