Starting phenix.real_space_refine on Sat Dec 28 00:49:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8t_15921/12_2024/8b8t_15921_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8t_15921/12_2024/8b8t_15921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b8t_15921/12_2024/8b8t_15921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8t_15921/12_2024/8b8t_15921.map" model { file = "/net/cci-nas-00/data/ceres_data/8b8t_15921/12_2024/8b8t_15921_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8t_15921/12_2024/8b8t_15921_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 4520 2.51 5 N 1202 2.21 5 O 1409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 7180 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1510 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 223} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 191 Chain: "E" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1898 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1887 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1885 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 4.84, per 1000 atoms: 0.67 Number of scatterers: 7180 At special positions: 0 Unit cell: (121.632, 98.826, 115.116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1409 8.00 N 1202 7.00 C 4520 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: 1.85 Conformation dependent library (CDL) restraints added in 1.3 seconds 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1872 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 7 sheets defined 32.5% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 288 through 301 removed outlier: 4.232A pdb=" N VAL A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 323 Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 351 through 363 Processing helix chain 'A' and resid 365 through 374 removed outlier: 3.506A pdb=" N ALA A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 removed outlier: 3.873A pdb=" N VAL A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 Processing helix chain 'A' and resid 421 through 434 removed outlier: 3.655A pdb=" N ALA A 433 " --> pdb=" O GLY A 429 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'A' and resid 455 through 470 Processing helix chain 'A' and resid 488 through 506 Processing helix chain 'A' and resid 513 through 523 Proline residue: A 518 - end of helix Processing helix chain 'E' and resid 9 through 20 removed outlier: 4.139A pdb=" N LYS E 13 " --> pdb=" O GLY E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 72 through 81 removed outlier: 3.878A pdb=" N CYS E 81 " --> pdb=" O LYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 153 removed outlier: 3.784A pdb=" N HIS E 153 " --> pdb=" O ARG E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 216 Processing helix chain 'E' and resid 217 through 222 Proline residue: E 220 - end of helix No H-bonds generated for 'chain 'E' and resid 217 through 222' Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.993A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.656A pdb=" N SER F 152 " --> pdb=" O CYS F 148 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 222 Proline residue: F 220 - end of helix No H-bonds generated for 'chain 'F' and resid 217 through 222' Processing helix chain 'G' and resid 8 through 20 removed outlier: 3.782A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 155 removed outlier: 4.313A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 217 removed outlier: 3.785A pdb=" N LYS G 217 " --> pdb=" O ASN G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 222 Processing sheet with id=AA1, first strand: chain 'E' and resid 59 through 62 removed outlier: 3.803A pdb=" N THR E 59 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL F 167 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 67 through 71 removed outlier: 3.634A pdb=" N ALA E 26 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU E 25 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET E 40 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N CYS E 27 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLN E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS E 240 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR E 224 " --> pdb=" O LYS E 240 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET E 229 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS E 135 " --> pdb=" O MET E 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 204 through 208 removed outlier: 5.384A pdb=" N ALA E 157 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER E 172 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN E 177 " --> pdb=" O GLU G 115 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN E 179 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL G 111 " --> pdb=" O LYS E 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 59 through 61 removed outlier: 3.746A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 25 through 30 removed outlier: 4.006A pdb=" N ALA F 26 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL F 70 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 34 through 40 removed outlier: 3.851A pdb=" N LEU F 47 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS F 246 " --> pdb=" O THR F 51 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY F 245 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL F 136 " --> pdb=" O GLU F 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 69 through 71 removed outlier: 6.885A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU G 37 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1176 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: 2.60 Time building geometry restraints manager: 2.15 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: 2029 1.33 - 1.46: 1068 1.46 - 1.58: 4101 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 7276 Sorted by residual: bond pdb=" CA PRO A 471 " pdb=" C PRO A 471 " ideal model delta sigma weight residual 1.514 1.545 -0.031 5.50e-03 3.31e+04 3.21e+01 bond pdb=" CA ILE A 517 " pdb=" CB ILE A 517 " ideal model delta sigma weight residual 1.539 1.521 0.018 5.40e-03 3.43e+04 1.12e+01 bond pdb=" CZ ARG F 91 " pdb=" NH2 ARG F 91 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.15e+00 bond pdb=" CZ ARG A 387 " pdb=" NH2 ARG A 387 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.08e+00 bond pdb=" CA PRO A 395 " pdb=" C PRO A 395 " ideal model delta sigma weight residual 1.517 1.544 -0.027 9.30e-03 1.16e+04 8.66e+00 ... (remaining 7271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 6759 1.74 - 3.49: 2609 3.49 - 5.23: 449 5.23 - 6.98: 53 6.98 - 8.72: 9 Bond angle restraints: 9879 Sorted by residual: angle pdb=" N PRO A 478 " pdb=" CA PRO A 478 " pdb=" CB PRO A 478 " ideal model delta sigma weight residual 103.17 108.99 -5.82 8.90e-01 1.26e+00 4.28e+01 angle pdb=" CA PHE G 215 " pdb=" CB PHE G 215 " pdb=" CG PHE G 215 " ideal model delta sigma weight residual 113.80 119.00 -5.20 1.00e+00 1.00e+00 2.70e+01 angle pdb=" C ASP F 243 " pdb=" N MET F 244 " pdb=" CA MET F 244 " ideal model delta sigma weight residual 120.29 127.48 -7.19 1.42e+00 4.96e-01 2.56e+01 angle pdb=" CB HIS E 246 " pdb=" CG HIS E 246 " pdb=" CD2 HIS E 246 " ideal model delta sigma weight residual 131.20 124.76 6.44 1.30e+00 5.92e-01 2.45e+01 angle pdb=" CA PHE A 296 " pdb=" CB PHE A 296 " pdb=" CG PHE A 296 " ideal model delta sigma weight residual 113.80 118.75 -4.95 1.00e+00 1.00e+00 2.45e+01 ... (remaining 9874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4085 17.88 - 35.76: 273 35.76 - 53.64: 57 53.64 - 71.51: 19 71.51 - 89.39: 8 Dihedral angle restraints: 4442 sinusoidal: 1571 harmonic: 2871 Sorted by residual: dihedral pdb=" C ASP F 243 " pdb=" N ASP F 243 " pdb=" CA ASP F 243 " pdb=" CB ASP F 243 " ideal model delta harmonic sigma weight residual -122.60 -136.27 13.67 0 2.50e+00 1.60e-01 2.99e+01 dihedral pdb=" CA GLY E 155 " pdb=" C GLY E 155 " pdb=" N ASP E 156 " pdb=" CA ASP E 156 " ideal model delta harmonic sigma weight residual -180.00 -152.69 -27.31 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" C ASN A 336 " pdb=" N ASN A 336 " pdb=" CA ASN A 336 " pdb=" CB ASN A 336 " ideal model delta harmonic sigma weight residual -122.60 -134.61 12.01 0 2.50e+00 1.60e-01 2.31e+01 ... (remaining 4439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 917 0.099 - 0.198: 251 0.198 - 0.296: 23 0.296 - 0.395: 6 0.395 - 0.494: 2 Chirality restraints: 1199 Sorted by residual: chirality pdb=" CA ASP F 243 " pdb=" N ASP F 243 " pdb=" C ASP F 243 " pdb=" CB ASP F 243 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA ASN A 336 " pdb=" N ASN A 336 " pdb=" C ASN A 336 " pdb=" CB ASN A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA THR E 219 " pdb=" N THR E 219 " pdb=" C THR E 219 " pdb=" CB THR E 219 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 1196 not shown) Planarity restraints: 1278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 211 " -0.114 2.00e-02 2.50e+03 6.11e-02 7.47e+01 pdb=" CG TYR F 211 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR F 211 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR F 211 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR F 211 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR F 211 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR F 211 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR F 211 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 28 " 0.092 2.00e-02 2.50e+03 4.90e-02 6.00e+01 pdb=" CG TRP F 28 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP F 28 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP F 28 " -0.062 2.00e-02 2.50e+03 pdb=" NE1 TRP F 28 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP F 28 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP F 28 " -0.069 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 28 " 0.047 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 28 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP F 28 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 211 " 0.097 2.00e-02 2.50e+03 5.10e-02 5.20e+01 pdb=" CG TYR G 211 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR G 211 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR G 211 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR G 211 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR G 211 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR G 211 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR G 211 " 0.073 2.00e-02 2.50e+03 ... (remaining 1275 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 3614 3.03 - 3.49: 7395 3.49 - 3.96: 10389 3.96 - 4.43: 10957 4.43 - 4.90: 19369 Nonbonded interactions: 51724 Sorted by model distance: nonbonded pdb=" OD2 ASP G 41 " pdb=" OG SER G 46 " model vdw 2.558 3.040 nonbonded pdb=" O ASN E 71 " pdb=" OG SER E 74 " model vdw 2.566 3.040 nonbonded pdb=" O LEU A 331 " pdb=" OG SER A 334 " model vdw 2.570 3.040 nonbonded pdb=" O THR G 216 " pdb=" OG1 THR G 219 " model vdw 2.579 3.040 nonbonded pdb=" OG SER F 134 " pdb=" OE2 GLU F 201 " model vdw 2.589 3.040 ... (remaining 51719 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 'E' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 28 or (resid 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 51 or (resid 52 and (n \ ame N or name CA or name C or name O or name CB )) or resid 53 through 107 or re \ sid 109 through 115 or (resid 116 and (name N or name CA or name C or name O or \ name CB )) or resid 117 through 127 or (resid 128 and (name N or name CA or name \ C or name O or name CB )) or resid 129 through 163 or (resid 164 through 165 an \ d (name N or name CA or name C or name O or name CB )) or resid 166 through 180 \ or (resid 181 and (name N or name CA or name C or name O or name CB )) or resid \ 182 through 185 or resid 193 through 228 or (resid 229 and (name N or name CA or \ name C or name O or name CB )) or resid 230 through 235 or (resid 236 and (name \ N or name CA or name C or name O or name CB )) or resid 237 or (resid 238 and ( \ name N or name CA or name C or name O or name CB )) or resid 239 or (resid 240 a \ nd (name N or name CA or name C or name O or name CB )) or resid 241 through 255 \ )) selection = (chain 'F' and (resid 1 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 11 or (resid 12 and (name N or name CA \ or name C or name O or name CB )) or resid 13 through 28 or (resid 29 and (name \ N or name CA or name C or name O or name CB )) or resid 30 through 39 or (resid \ 40 and (name N or name CA or name C or name O or name CB )) or resid 41 through \ 103 or (resid 104 through 105 and (name N or name CA or name C or name O or nam \ e CB )) or resid 106 through 110 or (resid 111 through 112 and (name N or name C \ A or name C or name O or name CB )) or resid 113 through 120 or (resid 121 throu \ gh 123 and (name N or name CA or name C or name O or name CB )) or resid 124 thr \ ough 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) \ or resid 153 through 160 or (resid 161 and (name N or name CA or name C or name \ O or name CB )) or resid 162 through 163 or (resid 164 through 165 and (name N o \ r name CA or name C or name O or name CB )) or resid 166 through 167 or (resid 1 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 169 through \ 185 or resid 193 through 255)) selection = (chain 'G' and (resid 1 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 39 or (resid 40 and (name N or name CA \ or name C or name O or name CB )) or resid 41 through 51 or (resid 52 and (name \ N or name CA or name C or name O or name CB )) or resid 53 through 106 or (resi \ d 107 and (name N or name CA or name C or name O or name CB )) or resid 109 thro \ ugh 110 or (resid 111 through 112 and (name N or name CA or name C or name O or \ name CB )) or resid 113 through 115 or (resid 116 and (name N or name CA or name \ C or name O or name CB )) or resid 117 through 120 or (resid 121 through 123 an \ d (name N or name CA or name C or name O or name CB )) or resid 124 through 127 \ or (resid 128 and (name N or name CA or name C or name O or name CB )) or resid \ 129 through 151 or (resid 152 and (name N or name CA or name C or name O or name \ CB )) or resid 153 through 160 or (resid 161 and (name N or name CA or name C o \ r name O or name CB )) or resid 162 through 167 or (resid 168 and (name N or nam \ e CA or name C or name O or name CB )) or resid 169 through 180 or (resid 181 an \ d (name N or name CA or name C or name O or name CB )) or resid 182 through 228 \ or (resid 229 and (name N or name CA or name C or name O or name CB )) or resid \ 230 through 235 or (resid 236 and (name N or name CA or name C or name O or name \ CB )) or resid 237 or (resid 238 and (name N or name CA or name C or name O or \ name CB )) or resid 239 or (resid 240 and (name N or name CA or name C or name O \ or name CB )) or resid 241 through 255)) } 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 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.970 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 : 0.011 0.046 7276 Z= 0.726 Angle : 1.782 8.724 9879 Z= 1.173 Chirality : 0.088 0.494 1199 Planarity : 0.013 0.112 1278 Dihedral : 14.331 89.392 2570 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.94 % Favored : 95.75 % Rotamer: Outliers : 1.78 % Allowed : 7.10 % Favored : 91.12 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 2.63 % 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 (0.25), residues: 965 helix: -0.89 (0.27), residues: 283 sheet: 0.47 (0.29), residues: 294 loop : -1.42 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.020 TRP F 28 HIS 0.017 0.004 HIS G 153 PHE 0.056 0.009 PHE A 441 TYR 0.114 0.024 TYR F 211 ARG 0.012 0.001 ARG E 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 408 PHE cc_start: 0.7673 (m-80) cc_final: 0.7179 (m-80) REVERT: A 441 PHE cc_start: 0.8098 (m-80) cc_final: 0.7817 (m-10) REVERT: A 465 GLN cc_start: 0.8503 (pm20) cc_final: 0.8233 (pm20) REVERT: E 1 MET cc_start: 0.5972 (tmm) cc_final: 0.4795 (tmm) REVERT: E 24 ASN cc_start: 0.8208 (m-40) cc_final: 0.7996 (m-40) REVERT: G 40 MET cc_start: 0.8316 (tpp) cc_final: 0.7809 (tpp) REVERT: G 49 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8366 (tt0) outliers start: 13 outliers final: 3 residues processed: 137 average time/residue: 0.2188 time to fit residues: 39.9714 Evaluate side-chains 95 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 184 GLN G 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7276 Z= 0.197 Angle : 0.655 7.254 9879 Z= 0.351 Chirality : 0.045 0.181 1199 Planarity : 0.004 0.036 1278 Dihedral : 4.754 21.283 1025 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.27 % Allowed : 4.23 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 965 helix: 1.10 (0.31), residues: 281 sheet: 0.93 (0.27), residues: 356 loop : -0.66 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 28 HIS 0.002 0.001 HIS F 44 PHE 0.016 0.001 PHE F 169 TYR 0.014 0.002 TYR G 239 ARG 0.003 0.001 ARG F 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.885 Fit side-chains REVERT: A 408 PHE cc_start: 0.7564 (m-80) cc_final: 0.7163 (m-80) REVERT: A 465 GLN cc_start: 0.8503 (pm20) cc_final: 0.8181 (pm20) REVERT: F 24 ASN cc_start: 0.8327 (t0) cc_final: 0.8033 (t0) REVERT: F 25 GLU cc_start: 0.7897 (mm-30) cc_final: 0.6926 (mm-30) REVERT: F 68 MET cc_start: 0.6624 (ppp) cc_final: 0.6382 (ppp) REVERT: G 21 ASP cc_start: 0.7313 (p0) cc_final: 0.6957 (p0) REVERT: G 25 GLU cc_start: 0.7871 (tp30) cc_final: 0.7507 (tt0) REVERT: G 119 MET cc_start: 0.6699 (pmm) cc_final: 0.5973 (pmm) REVERT: G 184 GLN cc_start: 0.7514 (tp-100) cc_final: 0.7301 (tp40) outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.2003 time to fit residues: 35.0189 Evaluate side-chains 91 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 59 optimal weight: 0.0670 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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: 0.7577 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7276 Z= 0.186 Angle : 0.606 8.140 9879 Z= 0.318 Chirality : 0.043 0.193 1199 Planarity : 0.004 0.034 1278 Dihedral : 4.316 20.043 1025 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.28), residues: 965 helix: 1.57 (0.32), residues: 280 sheet: 1.01 (0.27), residues: 356 loop : -0.58 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 28 HIS 0.004 0.001 HIS E 246 PHE 0.011 0.001 PHE G 207 TYR 0.015 0.002 TYR G 239 ARG 0.007 0.001 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.808 Fit side-chains REVERT: A 408 PHE cc_start: 0.7543 (m-80) cc_final: 0.7202 (m-80) REVERT: E 177 ASN cc_start: 0.7914 (t0) cc_final: 0.7674 (t0) REVERT: F 25 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7627 (tp30) REVERT: F 68 MET cc_start: 0.6653 (ppp) cc_final: 0.6453 (ppp) REVERT: G 21 ASP cc_start: 0.7155 (p0) cc_final: 0.6799 (p0) REVERT: G 119 MET cc_start: 0.6298 (pmm) cc_final: 0.5917 (pmm) REVERT: G 184 GLN cc_start: 0.7547 (tp-100) cc_final: 0.7132 (tp40) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1812 time to fit residues: 29.0272 Evaluate side-chains 87 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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: 0.7604 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7276 Z= 0.232 Angle : 0.622 8.447 9879 Z= 0.324 Chirality : 0.044 0.189 1199 Planarity : 0.004 0.030 1278 Dihedral : 4.398 19.725 1025 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.86 (0.28), residues: 965 helix: 1.59 (0.33), residues: 280 sheet: 0.83 (0.27), residues: 356 loop : -0.56 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 28 HIS 0.005 0.001 HIS G 246 PHE 0.017 0.002 PHE E 207 TYR 0.020 0.002 TYR G 239 ARG 0.003 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.904 Fit side-chains REVERT: E 24 ASN cc_start: 0.8292 (m-40) cc_final: 0.8029 (m-40) REVERT: E 175 LEU cc_start: 0.8354 (mp) cc_final: 0.8116 (mp) REVERT: E 177 ASN cc_start: 0.8046 (t0) cc_final: 0.7744 (t0) REVERT: E 244 MET cc_start: 0.8357 (tpp) cc_final: 0.8045 (tpp) REVERT: F 24 ASN cc_start: 0.8286 (t0) cc_final: 0.7971 (t0) REVERT: F 25 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7062 (tt0) REVERT: G 21 ASP cc_start: 0.7165 (p0) cc_final: 0.6809 (p0) REVERT: G 119 MET cc_start: 0.6263 (pmm) cc_final: 0.5890 (pmm) REVERT: G 184 GLN cc_start: 0.7672 (tp-100) cc_final: 0.7288 (tp40) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1822 time to fit residues: 28.4028 Evaluate side-chains 84 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.7603 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7276 Z= 0.222 Angle : 0.624 6.283 9879 Z= 0.321 Chirality : 0.044 0.186 1199 Planarity : 0.003 0.031 1278 Dihedral : 4.325 19.078 1025 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.87 (0.28), residues: 965 helix: 1.63 (0.33), residues: 280 sheet: 0.82 (0.27), residues: 356 loop : -0.54 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 28 HIS 0.004 0.001 HIS G 246 PHE 0.011 0.001 PHE F 169 TYR 0.019 0.002 TYR E 249 ARG 0.003 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.878 Fit side-chains REVERT: A 297 GLU cc_start: 0.6718 (pm20) cc_final: 0.6453 (pm20) REVERT: E 177 ASN cc_start: 0.8068 (t0) cc_final: 0.7775 (t0) REVERT: E 244 MET cc_start: 0.8274 (tpp) cc_final: 0.7973 (tpp) REVERT: F 24 ASN cc_start: 0.8292 (t0) cc_final: 0.7958 (t0) REVERT: F 25 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7089 (tt0) REVERT: F 150 ASP cc_start: 0.8216 (m-30) cc_final: 0.7932 (m-30) REVERT: G 21 ASP cc_start: 0.7142 (p0) cc_final: 0.6843 (p0) REVERT: G 119 MET cc_start: 0.6262 (pmm) cc_final: 0.5900 (pmm) REVERT: G 184 GLN cc_start: 0.7698 (tp-100) cc_final: 0.7266 (tp40) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1648 time to fit residues: 25.6758 Evaluate side-chains 85 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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: 0.7610 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7276 Z= 0.230 Angle : 0.632 6.811 9879 Z= 0.324 Chirality : 0.044 0.183 1199 Planarity : 0.003 0.029 1278 Dihedral : 4.309 19.212 1025 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.28), residues: 965 helix: 1.66 (0.33), residues: 280 sheet: 0.69 (0.26), residues: 354 loop : -0.60 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 28 HIS 0.004 0.001 HIS G 246 PHE 0.018 0.002 PHE A 441 TYR 0.017 0.002 TYR G 239 ARG 0.005 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.889 Fit side-chains REVERT: A 297 GLU cc_start: 0.6647 (pm20) cc_final: 0.6399 (pm20) REVERT: E 177 ASN cc_start: 0.8123 (t0) cc_final: 0.7830 (t0) REVERT: E 244 MET cc_start: 0.8192 (tpp) cc_final: 0.7909 (tpp) REVERT: F 24 ASN cc_start: 0.8268 (t0) cc_final: 0.7949 (t0) REVERT: F 25 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7116 (tt0) REVERT: G 21 ASP cc_start: 0.7194 (p0) cc_final: 0.6854 (p0) REVERT: G 119 MET cc_start: 0.6415 (pmm) cc_final: 0.6049 (pmm) REVERT: G 184 GLN cc_start: 0.7804 (tp-100) cc_final: 0.7290 (tp40) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2093 time to fit residues: 30.7976 Evaluate side-chains 87 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 68 optimal weight: 0.0970 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 246 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7276 Z= 0.260 Angle : 0.657 7.107 9879 Z= 0.337 Chirality : 0.045 0.193 1199 Planarity : 0.004 0.031 1278 Dihedral : 4.429 18.459 1025 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.28), residues: 965 helix: 1.61 (0.33), residues: 279 sheet: 0.62 (0.26), residues: 359 loop : -0.58 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 28 HIS 0.005 0.001 HIS G 246 PHE 0.024 0.002 PHE A 441 TYR 0.018 0.002 TYR G 239 ARG 0.004 0.001 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.944 Fit side-chains REVERT: A 465 GLN cc_start: 0.8097 (pm20) cc_final: 0.7692 (pm20) REVERT: E 177 ASN cc_start: 0.8147 (t0) cc_final: 0.7872 (t0) REVERT: E 244 MET cc_start: 0.8155 (tpp) cc_final: 0.7828 (tpp) REVERT: F 24 ASN cc_start: 0.8302 (t0) cc_final: 0.7975 (t0) REVERT: F 25 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7192 (tt0) REVERT: G 21 ASP cc_start: 0.7169 (p0) cc_final: 0.6840 (p0) REVERT: G 119 MET cc_start: 0.6430 (pmm) cc_final: 0.6073 (pmm) REVERT: G 184 GLN cc_start: 0.7871 (tp-100) cc_final: 0.7440 (tp40) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1669 time to fit residues: 24.2583 Evaluate side-chains 84 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.0000 chunk 59 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 246 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7276 Z= 0.182 Angle : 0.618 6.010 9879 Z= 0.315 Chirality : 0.044 0.186 1199 Planarity : 0.003 0.032 1278 Dihedral : 4.229 18.327 1025 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.79 (0.28), residues: 965 helix: 1.68 (0.33), residues: 279 sheet: 0.68 (0.27), residues: 356 loop : -0.57 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 28 HIS 0.003 0.001 HIS G 246 PHE 0.023 0.002 PHE A 441 TYR 0.017 0.001 TYR E 249 ARG 0.005 0.001 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.003 Fit side-chains REVERT: A 465 GLN cc_start: 0.8092 (pm20) cc_final: 0.7709 (pm20) REVERT: E 177 ASN cc_start: 0.8068 (t0) cc_final: 0.7777 (t0) REVERT: E 244 MET cc_start: 0.8136 (tpp) cc_final: 0.7932 (tpp) REVERT: F 70 VAL cc_start: 0.8923 (p) cc_final: 0.8489 (m) REVERT: G 21 ASP cc_start: 0.7059 (p0) cc_final: 0.6748 (p0) REVERT: G 184 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7416 (tp40) REVERT: G 250 TYR cc_start: 0.7832 (m-80) cc_final: 0.7574 (m-80) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1693 time to fit residues: 25.5557 Evaluate side-chains 88 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 246 HIS F 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7276 Z= 0.244 Angle : 0.649 6.362 9879 Z= 0.334 Chirality : 0.044 0.188 1199 Planarity : 0.004 0.032 1278 Dihedral : 4.324 18.349 1025 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.28), residues: 965 helix: 1.61 (0.33), residues: 279 sheet: 0.62 (0.27), residues: 359 loop : -0.57 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 28 HIS 0.004 0.001 HIS G 246 PHE 0.023 0.002 PHE A 441 TYR 0.017 0.002 TYR G 239 ARG 0.004 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.952 Fit side-chains REVERT: E 177 ASN cc_start: 0.8118 (t0) cc_final: 0.7843 (t0) REVERT: E 244 MET cc_start: 0.8115 (tpp) cc_final: 0.7909 (tpp) REVERT: F 24 ASN cc_start: 0.8285 (t0) cc_final: 0.7953 (t0) REVERT: F 25 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7238 (mm-30) REVERT: G 21 ASP cc_start: 0.7092 (p0) cc_final: 0.6812 (p0) REVERT: G 184 GLN cc_start: 0.7892 (tp-100) cc_final: 0.7454 (tp40) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1549 time to fit residues: 23.8340 Evaluate side-chains 87 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS E 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7276 Z= 0.291 Angle : 0.688 7.092 9879 Z= 0.355 Chirality : 0.045 0.189 1199 Planarity : 0.004 0.031 1278 Dihedral : 4.535 18.837 1025 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.62 (0.28), residues: 965 helix: 1.53 (0.33), residues: 279 sheet: 0.60 (0.26), residues: 359 loop : -0.71 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 28 HIS 0.006 0.001 HIS G 246 PHE 0.024 0.002 PHE A 441 TYR 0.019 0.002 TYR G 239 ARG 0.004 0.000 ARG G 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.971 Fit side-chains REVERT: E 177 ASN cc_start: 0.8173 (t0) cc_final: 0.7904 (t0) REVERT: E 244 MET cc_start: 0.8132 (tpp) cc_final: 0.7928 (tpp) REVERT: F 24 ASN cc_start: 0.8360 (t0) cc_final: 0.8055 (t0) REVERT: F 25 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7372 (mm-30) REVERT: F 131 GLN cc_start: 0.7889 (pp30) cc_final: 0.7633 (pp30) REVERT: G 21 ASP cc_start: 0.7172 (p0) cc_final: 0.6894 (p0) REVERT: G 184 GLN cc_start: 0.7981 (tp-100) cc_final: 0.7515 (tp40) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1689 time to fit residues: 24.8091 Evaluate side-chains 86 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.0670 chunk 70 optimal weight: 0.0670 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 246 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.128047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.105755 restraints weight = 15626.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.107006 restraints weight = 11378.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.107046 restraints weight = 10304.290| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7276 Z= 0.178 Angle : 0.626 6.833 9879 Z= 0.320 Chirality : 0.043 0.182 1199 Planarity : 0.003 0.032 1278 Dihedral : 4.148 17.600 1025 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.75 (0.28), residues: 965 helix: 1.61 (0.33), residues: 280 sheet: 0.73 (0.27), residues: 358 loop : -0.70 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 28 HIS 0.002 0.000 HIS E 246 PHE 0.022 0.002 PHE A 441 TYR 0.014 0.001 TYR E 249 ARG 0.005 0.001 ARG G 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1544.78 seconds wall clock time: 29 minutes 29.65 seconds (1769.65 seconds total)