Starting phenix.real_space_refine on Sat Dec 28 03:05:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pcq_13325/12_2024/7pcq_13325_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pcq_13325/12_2024/7pcq_13325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pcq_13325/12_2024/7pcq_13325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pcq_13325/12_2024/7pcq_13325.map" model { file = "/net/cci-nas-00/data/ceres_data/7pcq_13325/12_2024/7pcq_13325_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pcq_13325/12_2024/7pcq_13325_neut.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 Fe 4 7.16 5 S 22 5.16 5 C 4734 2.51 5 N 1246 2.21 5 O 1344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7350 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 1134 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Conformer: "B" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} bond proxies already assigned to first conformer: 1141 Chain: "C" Number of atoms: 1078 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Conformer: "B" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} bond proxies already assigned to first conformer: 1087 Chain: "D" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1111 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 138} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2786 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2777 Classifications: {'peptide': 337} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 324} Conformer: "B" Number of residues, atoms: 337, 2777 Classifications: {'peptide': 337} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 324} bond proxies already assigned to first conformer: 2823 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG B 104 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 104 " occ=0.50 residue: pdb=" N ALYS C 56 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS C 56 " occ=0.50 residue: pdb=" N ALYS E 232 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS E 232 " occ=0.50 Time building chain proxies: 7.92, per 1000 atoms: 1.08 Number of scatterers: 7350 At special positions: 0 Unit cell: (74.98, 99.104, 97.148, 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) Fe 4 26.01 S 22 16.00 O 1344 8.00 N 1246 7.00 C 4734 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.6 seconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 5 sheets defined 64.0% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 94 through 113 removed outlier: 3.619A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'B' and resid 4 through 18 removed outlier: 3.806A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 35 removed outlier: 3.637A pdb=" N GLY B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 57 through 77 Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.773A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N AARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 142 Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 90 removed outlier: 5.372A pdb=" N ALA C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 113 Processing helix chain 'C' and resid 118 through 137 Processing helix chain 'D' and resid 4 through 17 removed outlier: 3.730A pdb=" N LYS D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 36 through 46 removed outlier: 3.889A pdb=" N GLU D 43 " --> pdb=" O ARG D 40 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N SER D 44 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY D 46 " --> pdb=" O GLU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 57 Processing helix chain 'D' and resid 57 through 77 Processing helix chain 'D' and resid 81 through 95 removed outlier: 5.140A pdb=" N THR D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LEU D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 119 removed outlier: 3.781A pdb=" N PHE D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 123 through 142 Processing helix chain 'E' and resid 128 through 135 removed outlier: 4.049A pdb=" N LYS E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 169 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 269 through 285 Proline residue: E 281 - end of helix Processing helix chain 'E' and resid 287 through 302 removed outlier: 3.516A pdb=" N LYS E 297 " --> pdb=" O TYR E 293 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP E 300 " --> pdb=" O ASN E 296 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 332 removed outlier: 4.407A pdb=" N ALA E 308 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLU E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 365 Processing helix chain 'E' and resid 451 through 460 removed outlier: 3.747A pdb=" N LYS E 456 " --> pdb=" O GLU E 452 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 148 through 151 removed outlier: 5.814A pdb=" N GLY E 188 " --> pdb=" O PRO E 173 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG E 224 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU E 211 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N SER E 226 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE E 209 " --> pdb=" O SER E 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 153 through 156 removed outlier: 6.057A pdb=" N HIS E 241 " --> pdb=" O TRP E 195 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TRP E 195 " --> pdb=" O HIS E 241 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL E 200 " --> pdb=" O LEU E 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 153 through 156 Processing sheet with id=AA4, first strand: chain 'E' and resid 346 through 348 removed outlier: 4.126A pdb=" N ILE E 371 " --> pdb=" O THR E 348 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS E 368 " --> pdb=" O THR E 387 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR E 387 " --> pdb=" O LYS E 368 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU E 385 " --> pdb=" O PRO E 370 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER E 406 " --> pdb=" O THR E 415 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE E 417 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR E 404 " --> pdb=" O ILE E 417 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 350 through 353 removed outlier: 7.274A pdb=" N ASP E 428 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL E 397 " --> pdb=" O ASP E 428 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE E 430 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE E 395 " --> pdb=" O ILE E 430 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LYS E 432 " --> pdb=" O LYS E 393 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1340 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 2475 1.37 - 1.55: 5010 1.55 - 1.72: 14 1.72 - 1.90: 38 1.90 - 2.08: 16 Bond restraints: 7553 Sorted by residual: bond pdb=" CA SER E 169 " pdb=" CB SER E 169 " ideal model delta sigma weight residual 1.527 1.465 0.062 1.36e-02 5.41e+03 2.07e+01 bond pdb=" C VAL D 109 " pdb=" O VAL D 109 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.19e-02 7.06e+03 1.74e+01 bond pdb=" N VAL E 356 " pdb=" CA VAL E 356 " ideal model delta sigma weight residual 1.459 1.495 -0.037 9.10e-03 1.21e+04 1.62e+01 bond pdb=" N VAL E 234 " pdb=" CA VAL E 234 " ideal model delta sigma weight residual 1.456 1.496 -0.041 1.11e-02 8.12e+03 1.34e+01 bond pdb=" C3D HEM A 201 " pdb=" CAD HEM A 201 " ideal model delta sigma weight residual 1.544 1.472 0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 7548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 8730 2.27 - 4.53: 1486 4.53 - 6.80: 61 6.80 - 9.06: 5 9.06 - 11.33: 11 Bond angle restraints: 10293 Sorted by residual: angle pdb=" CA GLN D 127 " pdb=" C GLN D 127 " pdb=" O GLN D 127 " ideal model delta sigma weight residual 120.55 115.25 5.30 1.06e+00 8.90e-01 2.50e+01 angle pdb=" CA GLN B 127 " pdb=" C GLN B 127 " pdb=" O GLN B 127 " ideal model delta sigma weight residual 120.55 115.29 5.26 1.06e+00 8.90e-01 2.46e+01 angle pdb=" N ASP E 364 " pdb=" CA ASP E 364 " pdb=" C ASP E 364 " ideal model delta sigma weight residual 111.28 105.97 5.31 1.09e+00 8.42e-01 2.37e+01 angle pdb=" CA PHE C 43 " pdb=" C PHE C 43 " pdb=" N PRO C 44 " ideal model delta sigma weight residual 117.78 122.72 -4.94 1.06e+00 8.90e-01 2.17e+01 angle pdb=" CA PHE A 43 " pdb=" C PHE A 43 " pdb=" N PRO A 44 " ideal model delta sigma weight residual 117.78 122.69 -4.91 1.06e+00 8.90e-01 2.14e+01 ... (remaining 10288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4092 17.93 - 35.85: 263 35.85 - 53.78: 57 53.78 - 71.71: 10 71.71 - 89.63: 13 Dihedral angle restraints: 4435 sinusoidal: 1762 harmonic: 2673 Sorted by residual: dihedral pdb=" C2C HEM A 201 " pdb=" C3C HEM A 201 " pdb=" CAC HEM A 201 " pdb=" CBC HEM A 201 " ideal model delta sinusoidal sigma weight residual -0.00 -85.15 85.15 2 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" C2C HEM C 201 " pdb=" C3C HEM C 201 " pdb=" CAC HEM C 201 " pdb=" CBC HEM C 201 " ideal model delta sinusoidal sigma weight residual 0.00 -72.45 72.45 2 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" C2B HEM C 201 " pdb=" C3B HEM C 201 " pdb=" CAB HEM C 201 " pdb=" CBB HEM C 201 " ideal model delta sinusoidal sigma weight residual 180.00 109.92 70.08 2 1.00e+01 1.00e-02 4.24e+01 ... (remaining 4432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 505 0.062 - 0.123: 342 0.123 - 0.185: 219 0.185 - 0.246: 40 0.246 - 0.307: 8 Chirality restraints: 1114 Sorted by residual: chirality pdb=" CA VAL E 176 " pdb=" N VAL E 176 " pdb=" C VAL E 176 " pdb=" CB VAL E 176 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA ARG E 130 " pdb=" N ARG E 130 " pdb=" C ARG E 130 " pdb=" CB ARG E 130 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1111 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 231 " 0.027 2.00e-02 2.50e+03 5.45e-02 2.98e+01 pdb=" C THR E 231 " -0.094 2.00e-02 2.50e+03 pdb=" O THR E 231 " 0.035 2.00e-02 2.50e+03 pdb=" N BLYS E 232 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA AARG B 104 " -0.026 2.00e-02 2.50e+03 5.42e-02 2.93e+01 pdb=" C AARG B 104 " 0.094 2.00e-02 2.50e+03 pdb=" O AARG B 104 " -0.035 2.00e-02 2.50e+03 pdb=" N LEU B 105 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 266 " 0.026 2.00e-02 2.50e+03 5.33e-02 2.84e+01 pdb=" C LYS E 266 " -0.092 2.00e-02 2.50e+03 pdb=" O LYS E 266 " 0.034 2.00e-02 2.50e+03 pdb=" N PHE E 267 " 0.032 2.00e-02 2.50e+03 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 4121 3.03 - 3.49: 7699 3.49 - 3.96: 12608 3.96 - 4.43: 14872 4.43 - 4.90: 22478 Nonbonded interactions: 61778 Sorted by model distance: nonbonded pdb=" N THR A 118 " pdb=" O THR A 118 " model vdw 2.557 2.496 nonbonded pdb=" N THR C 118 " pdb=" O THR C 118 " model vdw 2.557 2.496 nonbonded pdb=" O TYR C 140 " pdb=" C ARG C 141 " model vdw 2.557 3.270 nonbonded pdb=" O TYR D 35 " pdb=" OG1 THR D 38 " model vdw 2.564 3.040 nonbonded pdb=" O TYR E 391 " pdb=" N HIS E 434 " model vdw 2.567 3.120 ... (remaining 61773 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' and (resid 1 through 55 or resid 57 through 141 or resid 201)) selection = (chain 'C' and (resid 1 through 55 or resid 57 through 141 or resid 201)) } ncs_group { reference = (chain 'B' and (resid 1 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 103 or resid 105 through 119 or (re \ sid 120 through 121 and (name N or name CA or name C or name O or name CB )) or \ resid 122 through 146 or resid 201)) selection = (chain 'D' and (resid 1 through 103 or resid 105 through 146 or resid 201)) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.140 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 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 : 0.013 0.089 7553 Z= 0.861 Angle : 1.548 11.328 10293 Z= 1.156 Chirality : 0.098 0.307 1114 Planarity : 0.008 0.055 1298 Dihedral : 13.616 89.634 2707 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.78 % Allowed : 5.58 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.72 (0.27), residues: 910 helix: 2.24 (0.22), residues: 525 sheet: -0.47 (0.57), residues: 78 loop : -0.33 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 14 HIS 0.005 0.001 HIS C 122 PHE 0.010 0.002 PHE E 225 TYR 0.015 0.002 TYR E 251 ARG 0.007 0.001 ARG E 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8609 (tt0) cc_final: 0.8055 (tt0) REVERT: A 39 THR cc_start: 0.8882 (p) cc_final: 0.7824 (p) REVERT: B 7 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8495 (mt-10) REVERT: B 35 TYR cc_start: 0.8799 (m-80) cc_final: 0.8596 (m-10) REVERT: B 47 ASP cc_start: 0.8397 (t0) cc_final: 0.8156 (t0) REVERT: B 98 VAL cc_start: 0.9513 (t) cc_final: 0.9114 (p) REVERT: B 105 LEU cc_start: 0.9260 (mt) cc_final: 0.9060 (mt) REVERT: B 108 ASN cc_start: 0.9230 (m-40) cc_final: 0.8907 (t0) REVERT: B 127 GLN cc_start: 0.8895 (tt0) cc_final: 0.8234 (tm-30) REVERT: B 131 GLN cc_start: 0.8995 (mm110) cc_final: 0.8478 (mm110) REVERT: C 14 TRP cc_start: 0.8183 (t-100) cc_final: 0.7827 (t-100) REVERT: D 31 LEU cc_start: 0.9406 (tp) cc_final: 0.9200 (tt) REVERT: D 38 THR cc_start: 0.8975 (p) cc_final: 0.8725 (p) outliers start: 5 outliers final: 2 residues processed: 175 average time/residue: 0.2505 time to fit residues: 56.9002 Evaluate side-chains 99 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS B 63 HIS B 102 ASN C 58 HIS ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7553 Z= 0.264 Angle : 0.625 6.489 10293 Z= 0.323 Chirality : 0.042 0.147 1114 Planarity : 0.004 0.038 1298 Dihedral : 8.714 89.030 1007 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.69 % Allowed : 13.25 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.27), residues: 910 helix: 2.79 (0.22), residues: 521 sheet: 0.36 (0.57), residues: 81 loop : 0.23 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 14 HIS 0.004 0.001 HIS E 369 PHE 0.016 0.002 PHE E 178 TYR 0.010 0.001 TYR B 130 ARG 0.006 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8694 (tt0) cc_final: 0.8317 (tt0) REVERT: B 7 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8645 (mt-10) REVERT: B 21 ASP cc_start: 0.8534 (p0) cc_final: 0.5376 (p0) REVERT: B 99 ASP cc_start: 0.8929 (t0) cc_final: 0.8541 (t0) REVERT: B 101 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8355 (mp0) REVERT: B 127 GLN cc_start: 0.9062 (tt0) cc_final: 0.8452 (tm-30) REVERT: B 131 GLN cc_start: 0.9110 (mm110) cc_final: 0.8807 (mm110) REVERT: D 132 LYS cc_start: 0.9154 (mtpt) cc_final: 0.8921 (mtpp) REVERT: E 155 MET cc_start: 0.8254 (mmm) cc_final: 0.8028 (mmp) REVERT: E 254 MET cc_start: 0.7928 (ttt) cc_final: 0.7726 (ttt) outliers start: 12 outliers final: 8 residues processed: 109 average time/residue: 0.2124 time to fit residues: 31.2749 Evaluate side-chains 85 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 63 HIS B 108 ASN C 122 HIS D 39 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7553 Z= 0.265 Angle : 0.620 8.778 10293 Z= 0.310 Chirality : 0.041 0.152 1114 Planarity : 0.004 0.042 1298 Dihedral : 8.526 89.163 1006 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.34 % Allowed : 12.47 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.28), residues: 910 helix: 2.67 (0.22), residues: 523 sheet: 0.40 (0.53), residues: 97 loop : 0.43 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 14 HIS 0.004 0.001 HIS D 143 PHE 0.013 0.001 PHE E 178 TYR 0.011 0.001 TYR B 35 ARG 0.003 0.001 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8699 (mt-10) REVERT: B 21 ASP cc_start: 0.7909 (p0) cc_final: 0.6297 (p0) REVERT: B 127 GLN cc_start: 0.9123 (tt0) cc_final: 0.8472 (tm-30) REVERT: B 131 GLN cc_start: 0.9040 (mm110) cc_final: 0.8700 (mm110) REVERT: C 68 ASN cc_start: 0.8712 (t0) cc_final: 0.8466 (t0) REVERT: D 101 GLU cc_start: 0.7992 (tp30) cc_final: 0.7631 (tp30) REVERT: D 104 ARG cc_start: 0.9003 (mtm110) cc_final: 0.8562 (ptm-80) REVERT: E 124 MET cc_start: 0.5829 (tpt) cc_final: 0.5611 (mmm) REVERT: E 155 MET cc_start: 0.8244 (mmm) cc_final: 0.7972 (mmp) outliers start: 17 outliers final: 11 residues processed: 95 average time/residue: 0.2102 time to fit residues: 27.3404 Evaluate side-chains 85 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 77 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 39 GLN B 63 HIS B 108 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7553 Z= 0.211 Angle : 0.610 9.604 10293 Z= 0.303 Chirality : 0.040 0.166 1114 Planarity : 0.004 0.040 1298 Dihedral : 8.454 84.571 1006 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.82 % Allowed : 13.38 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.28), residues: 910 helix: 2.88 (0.22), residues: 509 sheet: 0.22 (0.53), residues: 102 loop : 0.46 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 14 HIS 0.004 0.001 HIS C 89 PHE 0.016 0.001 PHE E 418 TYR 0.011 0.001 TYR B 35 ARG 0.007 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8646 (mt-10) REVERT: B 21 ASP cc_start: 0.7855 (p0) cc_final: 0.6429 (p0) REVERT: B 39 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8509 (pt0) REVERT: B 127 GLN cc_start: 0.9091 (tt0) cc_final: 0.8443 (tm-30) REVERT: C 68 ASN cc_start: 0.8718 (t0) cc_final: 0.8473 (t0) REVERT: D 99 ASP cc_start: 0.8324 (t0) cc_final: 0.8092 (t0) REVERT: D 132 LYS cc_start: 0.9209 (mtpt) cc_final: 0.8961 (mtpp) REVERT: E 124 MET cc_start: 0.5869 (tpt) cc_final: 0.5662 (mmm) REVERT: E 392 TRP cc_start: 0.8866 (m100) cc_final: 0.8556 (m100) REVERT: E 396 MET cc_start: 0.8824 (tpp) cc_final: 0.8576 (tpp) outliers start: 13 outliers final: 8 residues processed: 94 average time/residue: 0.2045 time to fit residues: 26.2815 Evaluate side-chains 85 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 7553 Z= 0.331 Angle : 0.646 8.495 10293 Z= 0.318 Chirality : 0.040 0.221 1114 Planarity : 0.004 0.043 1298 Dihedral : 8.589 87.987 1006 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.82 % Allowed : 13.77 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.28), residues: 910 helix: 2.84 (0.22), residues: 509 sheet: 0.44 (0.55), residues: 98 loop : 0.55 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 15 HIS 0.004 0.001 HIS C 103 PHE 0.016 0.001 PHE E 178 TYR 0.018 0.001 TYR B 35 ARG 0.005 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8516 (mmm-85) REVERT: B 7 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8536 (mt-10) REVERT: B 21 ASP cc_start: 0.7904 (p0) cc_final: 0.5657 (p0) REVERT: B 127 GLN cc_start: 0.9134 (tt0) cc_final: 0.8487 (tm-30) REVERT: B 131 GLN cc_start: 0.9031 (mm110) cc_final: 0.8709 (mm-40) REVERT: C 68 ASN cc_start: 0.8762 (t0) cc_final: 0.8545 (t0) REVERT: D 132 LYS cc_start: 0.9264 (mtpt) cc_final: 0.9056 (mtpp) outliers start: 13 outliers final: 11 residues processed: 86 average time/residue: 0.2220 time to fit residues: 25.9340 Evaluate side-chains 83 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 112 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 6.9990 chunk 21 optimal weight: 0.0570 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.0170 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 63 HIS ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7553 Z= 0.206 Angle : 0.648 10.820 10293 Z= 0.319 Chirality : 0.041 0.264 1114 Planarity : 0.004 0.041 1298 Dihedral : 8.437 88.719 1004 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.82 % Allowed : 14.42 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.28), residues: 910 helix: 2.74 (0.22), residues: 521 sheet: 0.50 (0.55), residues: 98 loop : 0.30 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.003 0.001 HIS C 103 PHE 0.018 0.001 PHE E 418 TYR 0.013 0.001 TYR B 35 ARG 0.007 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8569 (mt-10) REVERT: B 127 GLN cc_start: 0.9062 (tt0) cc_final: 0.8412 (tm-30) REVERT: C 68 ASN cc_start: 0.8741 (t0) cc_final: 0.8532 (t0) REVERT: E 392 TRP cc_start: 0.8872 (m100) cc_final: 0.8563 (m100) REVERT: E 396 MET cc_start: 0.8771 (tpp) cc_final: 0.8522 (tpp) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.2091 time to fit residues: 26.1219 Evaluate side-chains 84 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 85 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7553 Z= 0.233 Angle : 0.670 10.750 10293 Z= 0.328 Chirality : 0.041 0.247 1114 Planarity : 0.004 0.042 1298 Dihedral : 8.412 88.531 1004 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.56 % Allowed : 14.68 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.28), residues: 910 helix: 2.67 (0.22), residues: 523 sheet: 0.56 (0.56), residues: 92 loop : 0.24 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.003 0.001 HIS D 117 PHE 0.017 0.001 PHE E 418 TYR 0.011 0.001 TYR B 35 ARG 0.006 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8523 (mt-10) REVERT: B 127 GLN cc_start: 0.9085 (tt0) cc_final: 0.8412 (tm-30) REVERT: B 131 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8513 (mm110) REVERT: C 68 ASN cc_start: 0.8761 (t0) cc_final: 0.8553 (t0) REVERT: C 116 GLU cc_start: 0.7852 (pm20) cc_final: 0.7637 (pm20) REVERT: E 124 MET cc_start: 0.5541 (mmm) cc_final: 0.4509 (tmm) REVERT: E 396 MET cc_start: 0.8759 (tpp) cc_final: 0.8543 (tpp) outliers start: 11 outliers final: 10 residues processed: 84 average time/residue: 0.2114 time to fit residues: 24.2943 Evaluate side-chains 82 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 67 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7553 Z= 0.234 Angle : 0.676 10.669 10293 Z= 0.334 Chirality : 0.041 0.252 1114 Planarity : 0.004 0.041 1298 Dihedral : 8.238 86.051 1004 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.82 % Allowed : 15.19 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.28), residues: 910 helix: 2.63 (0.22), residues: 523 sheet: 0.53 (0.56), residues: 92 loop : 0.20 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.004 0.001 HIS A 87 PHE 0.014 0.001 PHE E 418 TYR 0.011 0.001 TYR B 35 ARG 0.008 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8530 (mt-10) REVERT: B 121 GLU cc_start: 0.8438 (tp30) cc_final: 0.8167 (tp30) REVERT: B 127 GLN cc_start: 0.9100 (tt0) cc_final: 0.8420 (tm-30) REVERT: B 131 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8523 (mm110) REVERT: C 68 ASN cc_start: 0.8780 (t0) cc_final: 0.8573 (t0) REVERT: E 124 MET cc_start: 0.5708 (mmm) cc_final: 0.5099 (tmm) REVERT: E 382 MET cc_start: 0.7893 (mpp) cc_final: 0.7616 (mpp) outliers start: 13 outliers final: 11 residues processed: 79 average time/residue: 0.2184 time to fit residues: 23.5529 Evaluate side-chains 82 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 24 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7553 Z= 0.238 Angle : 0.674 11.144 10293 Z= 0.334 Chirality : 0.041 0.210 1114 Planarity : 0.004 0.039 1298 Dihedral : 8.192 86.336 1004 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.69 % Allowed : 15.32 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.28), residues: 910 helix: 2.68 (0.22), residues: 513 sheet: 0.46 (0.56), residues: 92 loop : 0.12 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.005 0.001 HIS D 92 PHE 0.016 0.001 PHE C 33 TYR 0.010 0.001 TYR B 35 ARG 0.008 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8527 (mt-10) REVERT: B 121 GLU cc_start: 0.8447 (tp30) cc_final: 0.8176 (tp30) REVERT: B 127 GLN cc_start: 0.9101 (tt0) cc_final: 0.8435 (tm-30) REVERT: B 131 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8520 (mm110) REVERT: E 382 MET cc_start: 0.7959 (mpp) cc_final: 0.7749 (mpp) REVERT: E 396 MET cc_start: 0.8661 (mmp) cc_final: 0.8276 (tpp) outliers start: 12 outliers final: 10 residues processed: 81 average time/residue: 0.2090 time to fit residues: 23.2142 Evaluate side-chains 81 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 54 optimal weight: 0.0870 chunk 43 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7553 Z= 0.297 Angle : 0.713 11.172 10293 Z= 0.352 Chirality : 0.042 0.242 1114 Planarity : 0.004 0.038 1298 Dihedral : 8.242 87.159 1004 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.69 % Allowed : 15.58 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.28), residues: 910 helix: 2.69 (0.22), residues: 513 sheet: 0.48 (0.57), residues: 92 loop : 0.14 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.004 0.001 HIS D 92 PHE 0.013 0.001 PHE C 33 TYR 0.010 0.001 TYR B 35 ARG 0.009 0.001 ARG E 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8535 (mt-10) REVERT: B 121 GLU cc_start: 0.8483 (tp30) cc_final: 0.8221 (tp30) REVERT: B 127 GLN cc_start: 0.9133 (tt0) cc_final: 0.8465 (tm-30) REVERT: B 131 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8554 (mm110) REVERT: E 396 MET cc_start: 0.8691 (mmp) cc_final: 0.8328 (tpp) outliers start: 12 outliers final: 11 residues processed: 79 average time/residue: 0.2203 time to fit residues: 24.1457 Evaluate side-chains 84 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.2980 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 62 optimal weight: 0.2980 chunk 4 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** 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 = 0.2746 r_free = 0.2746 target = 0.030548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2330 r_free = 0.2330 target = 0.020497 restraints weight = 168005.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.021961 restraints weight = 57597.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.023015 restraints weight = 32444.481| |-----------------------------------------------------------------------------| r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2413 r_free = 0.2413 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2407 r_free = 0.2407 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7553 Z= 0.232 Angle : 0.689 11.305 10293 Z= 0.343 Chirality : 0.041 0.236 1114 Planarity : 0.004 0.039 1298 Dihedral : 8.181 87.631 1004 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.43 % Allowed : 15.97 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.28), residues: 910 helix: 2.65 (0.22), residues: 513 sheet: 0.48 (0.56), residues: 92 loop : 0.13 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.003 0.001 HIS C 87 PHE 0.015 0.001 PHE C 33 TYR 0.010 0.001 TYR B 35 ARG 0.009 0.001 ARG E 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1831.55 seconds wall clock time: 34 minutes 31.45 seconds (2071.45 seconds total)