Starting phenix.real_space_refine on Tue Dec 31 15:12:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7enn_31217/12_2024/7enn_31217.cif Found real_map, /net/cci-nas-00/data/ceres_data/7enn_31217/12_2024/7enn_31217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7enn_31217/12_2024/7enn_31217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7enn_31217/12_2024/7enn_31217.map" model { file = "/net/cci-nas-00/data/ceres_data/7enn_31217/12_2024/7enn_31217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7enn_31217/12_2024/7enn_31217.cif" } resolution = 2.8 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= 0.001 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: 7 Type Number sf(0) Gaussians P 294 5.49 5 S 31 5.16 5 Be 1 3.05 5 C 9365 2.51 5 N 2989 2.21 5 O 3636 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16319 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 4315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4315 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 14, 'TRANS': 524} Chain breaks: 4 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2978 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3008 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.70, per 1000 atoms: 0.66 Number of scatterers: 16319 At special positions: 0 Unit cell: (143.431, 126.652, 115.286, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 31 16.00 P 294 15.00 F 3 9.00 O 3636 8.00 N 2989 7.00 C 9365 6.00 Be 1 4.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.29 Conformation dependent library (CDL) restraints added in 1.4 seconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 63.5% alpha, 5.4% beta 145 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 6.91 Creating SS restraints... Processing helix chain 'K' and resid 32 through 40 removed outlier: 3.711A pdb=" N LEU K 36 " --> pdb=" O GLN K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 64 Processing helix chain 'K' and resid 76 through 91 Processing helix chain 'K' and resid 103 through 105 No H-bonds generated for 'chain 'K' and resid 103 through 105' Processing helix chain 'K' and resid 106 through 118 removed outlier: 3.576A pdb=" N GLN K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 138 Processing helix chain 'K' and resid 153 through 159 Processing helix chain 'K' and resid 161 through 165 Processing helix chain 'K' and resid 175 through 179 Processing helix chain 'K' and resid 184 through 192 removed outlier: 3.750A pdb=" N GLU K 192 " --> pdb=" O LYS K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 221 Processing helix chain 'K' and resid 226 through 228 No H-bonds generated for 'chain 'K' and resid 226 through 228' Processing helix chain 'K' and resid 229 through 237 removed outlier: 3.560A pdb=" N TYR K 237 " --> pdb=" O PHE K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 254 removed outlier: 3.867A pdb=" N GLU K 249 " --> pdb=" O GLU K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 296 Processing helix chain 'K' and resid 313 through 324 removed outlier: 3.947A pdb=" N GLN K 317 " --> pdb=" O ASN K 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 332 removed outlier: 4.781A pdb=" N ASP K 329 " --> pdb=" O TYR K 326 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY K 330 " --> pdb=" O LEU K 327 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL K 331 " --> pdb=" O PHE K 328 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU K 332 " --> pdb=" O ASP K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 363 Processing helix chain 'K' and resid 372 through 387 removed outlier: 3.511A pdb=" N LEU K 376 " --> pdb=" O MET K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 399 through 412 removed outlier: 3.943A pdb=" N HIS K 403 " --> pdb=" O GLY K 399 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY K 410 " --> pdb=" O ILE K 406 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN K 412 " --> pdb=" O ASN K 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 421 through 425 Processing helix chain 'K' and resid 444 through 454 removed outlier: 4.237A pdb=" N ASP K 448 " --> pdb=" O ASN K 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 488 removed outlier: 3.562A pdb=" N ILE K 478 " --> pdb=" O THR K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 489 through 498 removed outlier: 3.931A pdb=" N ILE K 493 " --> pdb=" O LEU K 489 " (cutoff:3.500A) Processing helix chain 'K' and resid 536 through 545 removed outlier: 3.964A pdb=" N SER K 540 " --> pdb=" O ILE K 536 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU K 542 " --> pdb=" O LEU K 538 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY K 543 " --> pdb=" O GLU K 539 " (cutoff:3.500A) Processing helix chain 'K' and resid 586 through 599 Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.590A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'L' and resid 24 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 3.762A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA L 76 " --> pdb=" O TYR L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 removed outlier: 3.507A pdb=" N VAL L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.618A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.552A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.749A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.559A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.721A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.556A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing sheet with id=AA1, first strand: chain 'K' and resid 123 through 125 removed outlier: 6.289A pdb=" N VAL K 124 " --> pdb=" O LEU K 150 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR K 152 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE K 98 " --> pdb=" O LEU K 149 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N THR K 151 " --> pdb=" O PHE K 98 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE K 100 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU K 99 " --> pdb=" O VAL K 172 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU K 171 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU K 201 " --> pdb=" O LEU K 171 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL K 173 " --> pdb=" O LEU K 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 390 through 393 removed outlier: 6.163A pdb=" N GLU K 391 " --> pdb=" O LEU K 418 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N SER K 420 " --> pdb=" O GLU K 391 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL K 393 " --> pdb=" O SER K 420 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL K 366 " --> pdb=" O PHE K 417 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU K 419 " --> pdb=" O VAL K 366 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU K 368 " --> pdb=" O LEU K 419 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL K 436 " --> pdb=" O ILE K 467 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LEU K 469 " --> pdb=" O VAL K 436 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE K 438 " --> pdb=" O LEU K 469 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY K 471 " --> pdb=" O PHE K 438 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS K 280 " --> pdb=" O ILE K 470 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.754A pdb=" N ARG A 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'L' and resid 96 through 98 removed outlier: 6.556A pdb=" N THR L 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.105A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.727A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.719A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.311A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 574 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 8.56 Time building geometry restraints manager: 4.95 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: 3473 1.33 - 1.45: 4922 1.45 - 1.57: 8170 1.57 - 1.69: 586 1.69 - 1.81: 54 Bond restraints: 17205 Sorted by residual: bond pdb=" F2 BEF K 902 " pdb="BE BEF K 902 " ideal model delta sigma weight residual 1.476 1.705 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" F1 BEF K 902 " pdb="BE BEF K 902 " ideal model delta sigma weight residual 1.476 1.700 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" F3 BEF K 902 " pdb="BE BEF K 902 " ideal model delta sigma weight residual 1.476 1.690 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" CA GLN K 207 " pdb=" C GLN K 207 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.34e-02 5.57e+03 2.90e+00 bond pdb=" CA GLU K 334 " pdb=" CB GLU K 334 " ideal model delta sigma weight residual 1.525 1.538 -0.014 8.30e-03 1.45e+04 2.75e+00 ... (remaining 17200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 24442 4.21 - 8.42: 37 8.42 - 12.64: 3 12.64 - 16.85: 1 16.85 - 21.06: 1 Bond angle restraints: 24484 Sorted by residual: angle pdb=" F1 BEF K 902 " pdb="BE BEF K 902 " pdb=" F3 BEF K 902 " ideal model delta sigma weight residual 120.12 99.06 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" F2 BEF K 902 " pdb="BE BEF K 902 " pdb=" F3 BEF K 902 " ideal model delta sigma weight residual 119.96 105.13 14.83 3.00e+00 1.11e-01 2.44e+01 angle pdb=" C VAL K 397 " pdb=" N ARG K 398 " pdb=" CA ARG K 398 " ideal model delta sigma weight residual 121.54 129.93 -8.39 1.91e+00 2.74e-01 1.93e+01 angle pdb=" N LEU K 522 " pdb=" CA LEU K 522 " pdb=" C LEU K 522 " ideal model delta sigma weight residual 111.81 106.27 5.54 1.54e+00 4.22e-01 1.29e+01 angle pdb=" C PRO K 333 " pdb=" N GLU K 334 " pdb=" CA GLU K 334 " ideal model delta sigma weight residual 124.21 128.50 -4.29 1.21e+00 6.83e-01 1.26e+01 ... (remaining 24479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 8134 35.15 - 70.31: 1435 70.31 - 105.46: 9 105.46 - 140.61: 3 140.61 - 175.77: 3 Dihedral angle restraints: 9584 sinusoidal: 5825 harmonic: 3759 Sorted by residual: dihedral pdb=" C5' ADP K 901 " pdb=" O5' ADP K 901 " pdb=" PA ADP K 901 " pdb=" O2A ADP K 901 " ideal model delta sinusoidal sigma weight residual -60.00 115.77 -175.77 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP K 901 " pdb=" O3A ADP K 901 " pdb=" PA ADP K 901 " pdb=" PB ADP K 901 " ideal model delta sinusoidal sigma weight residual -60.00 65.01 -125.01 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" O1B ADP K 901 " pdb=" O3A ADP K 901 " pdb=" PB ADP K 901 " pdb=" PA ADP K 901 " ideal model delta sinusoidal sigma weight residual -60.00 58.31 -118.31 1 2.00e+01 2.50e-03 3.54e+01 ... (remaining 9581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1879 0.036 - 0.072: 725 0.072 - 0.108: 142 0.108 - 0.144: 23 0.144 - 0.180: 3 Chirality restraints: 2772 Sorted by residual: chirality pdb=" CB ILE H 91 " pdb=" CA ILE H 91 " pdb=" CG1 ILE H 91 " pdb=" CG2 ILE H 91 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CB VAL K 596 " pdb=" CA VAL K 596 " pdb=" CG1 VAL K 596 " pdb=" CG2 VAL K 596 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" C3' ADP K 901 " pdb=" C2' ADP K 901 " pdb=" C4' ADP K 901 " pdb=" O3' ADP K 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 2769 not shown) Planarity restraints: 2097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN K 444 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO K 445 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 445 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 445 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 168 " 0.012 2.00e-02 2.50e+03 1.18e-02 3.46e+00 pdb=" CG TRP K 168 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP K 168 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP K 168 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP K 168 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP K 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 168 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 168 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 168 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP K 168 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 517 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C ILE K 517 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE K 517 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU K 518 " 0.011 2.00e-02 2.50e+03 ... (remaining 2094 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 452 2.68 - 3.24: 14197 3.24 - 3.79: 28708 3.79 - 4.35: 38713 4.35 - 4.90: 56736 Nonbonded interactions: 138806 Sorted by model distance: nonbonded pdb=" N2 DG I 13 " pdb=" O2 DC J 135 " model vdw 2.127 2.496 nonbonded pdb=" OH TYR K 153 " pdb=" O ASP K 174 " model vdw 2.170 3.040 nonbonded pdb=" OH TYR K 214 " pdb=" O SER K 226 " model vdw 2.179 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.190 3.040 nonbonded pdb=" O SER K 244 " pdb=" OG SER K 248 " model vdw 2.205 3.040 ... (remaining 138801 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } ncs_group { reference = (chain 'F' and resid 23 through 101) selection = (chain 'L' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.960 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: 0.840 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 45.110 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.006 0.229 17205 Z= 0.332 Angle : 0.683 21.061 24484 Z= 0.403 Chirality : 0.038 0.180 2772 Planarity : 0.004 0.049 2097 Dihedral : 25.221 175.768 7160 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.23), residues: 1274 helix: 1.02 (0.18), residues: 789 sheet: -0.83 (0.64), residues: 80 loop : -2.24 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP K 168 HIS 0.003 0.001 HIS L 75 PHE 0.015 0.002 PHE K 409 TYR 0.023 0.002 TYR G 50 ARG 0.013 0.001 ARG K 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.299 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 2.0810 time to fit residues: 457.4592 Evaluate side-chains 161 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 429 ASN K 447 ASN K 491 ASN L 93 GLN D 44 GLN D 46 HIS F 93 GLN H 46 HIS H 81 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17205 Z= 0.209 Angle : 0.585 9.209 24484 Z= 0.339 Chirality : 0.036 0.142 2772 Planarity : 0.004 0.040 2097 Dihedral : 28.703 167.358 4627 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.92 % Allowed : 9.88 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.24), residues: 1274 helix: 1.59 (0.18), residues: 793 sheet: -0.26 (0.67), residues: 75 loop : -1.99 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 39 HIS 0.003 0.001 HIS K 147 PHE 0.020 0.001 PHE K 409 TYR 0.012 0.001 TYR K 385 ARG 0.010 0.000 ARG K 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 1.229 Fit side-chains REVERT: K 398 ARG cc_start: 0.7377 (mmm160) cc_final: 0.7102 (mmm160) REVERT: C 92 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: D 76 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.8006 (ptp90) REVERT: D 90 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7816 (mt-10) outliers start: 21 outliers final: 6 residues processed: 195 average time/residue: 1.9031 time to fit residues: 399.0380 Evaluate side-chains 179 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 123 optimal weight: 0.0980 chunk 138 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS D 60 ASN H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17205 Z= 0.293 Angle : 0.594 9.094 24484 Z= 0.344 Chirality : 0.037 0.141 2772 Planarity : 0.004 0.042 2097 Dihedral : 28.789 173.319 4627 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.47 % Allowed : 10.61 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1274 helix: 1.78 (0.18), residues: 791 sheet: -0.48 (0.66), residues: 80 loop : -1.80 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 39 HIS 0.003 0.001 HIS F 75 PHE 0.022 0.001 PHE K 409 TYR 0.013 0.001 TYR F 51 ARG 0.006 0.000 ARG K 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.360 Fit side-chains REVERT: K 374 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8069 (mm-40) REVERT: C 64 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7637 (tp30) REVERT: C 92 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: D 76 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.8029 (ptp90) REVERT: G 64 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7461 (tp30) outliers start: 27 outliers final: 13 residues processed: 182 average time/residue: 1.9801 time to fit residues: 387.8904 Evaluate side-chains 187 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17205 Z= 0.248 Angle : 0.586 9.010 24484 Z= 0.340 Chirality : 0.036 0.143 2772 Planarity : 0.004 0.042 2097 Dihedral : 28.779 172.287 4627 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.83 % Allowed : 11.71 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.24), residues: 1274 helix: 1.86 (0.18), residues: 791 sheet: -0.34 (0.66), residues: 80 loop : -1.74 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 39 HIS 0.003 0.001 HIS F 75 PHE 0.021 0.001 PHE K 409 TYR 0.012 0.001 TYR F 51 ARG 0.006 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.526 Fit side-chains REVERT: K 374 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8056 (mm-40) REVERT: C 64 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: C 92 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7668 (mt-10) outliers start: 20 outliers final: 11 residues processed: 174 average time/residue: 1.8961 time to fit residues: 354.6840 Evaluate side-chains 181 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.0060 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17205 Z= 0.186 Angle : 0.583 11.088 24484 Z= 0.337 Chirality : 0.035 0.143 2772 Planarity : 0.004 0.062 2097 Dihedral : 28.774 171.664 4627 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.56 % Allowed : 12.63 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.24), residues: 1274 helix: 1.94 (0.18), residues: 793 sheet: -0.31 (0.66), residues: 80 loop : -1.70 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 39 HIS 0.003 0.001 HIS L 18 PHE 0.018 0.001 PHE K 409 TYR 0.011 0.001 TYR F 51 ARG 0.006 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 1.528 Fit side-chains REVERT: K 374 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8061 (mm-40) REVERT: C 64 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: C 92 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7641 (mt-10) outliers start: 17 outliers final: 10 residues processed: 176 average time/residue: 1.9649 time to fit residues: 371.2103 Evaluate side-chains 180 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 142 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17205 Z= 0.194 Angle : 0.578 10.479 24484 Z= 0.335 Chirality : 0.035 0.141 2772 Planarity : 0.004 0.036 2097 Dihedral : 28.743 171.739 4627 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.20 % Allowed : 12.72 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1274 helix: 1.99 (0.18), residues: 793 sheet: -0.26 (0.66), residues: 80 loop : -1.66 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 39 HIS 0.003 0.001 HIS L 18 PHE 0.015 0.001 PHE K 409 TYR 0.010 0.001 TYR F 51 ARG 0.006 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 1.506 Fit side-chains REVERT: K 374 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8089 (mm-40) REVERT: C 64 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: C 92 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: D 90 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: G 64 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7438 (tp30) outliers start: 24 outliers final: 10 residues processed: 177 average time/residue: 1.9834 time to fit residues: 381.6495 Evaluate side-chains 181 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 372 MET Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17205 Z= 0.200 Angle : 0.556 10.241 24484 Z= 0.323 Chirality : 0.035 0.139 2772 Planarity : 0.003 0.037 2097 Dihedral : 28.588 171.047 4627 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.65 % Allowed : 13.91 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1274 helix: 2.17 (0.18), residues: 787 sheet: -0.16 (0.65), residues: 80 loop : -1.48 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 39 HIS 0.003 0.001 HIS L 18 PHE 0.013 0.001 PHE K 409 TYR 0.010 0.001 TYR K 214 ARG 0.008 0.000 ARG K 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: K 398 ARG cc_start: 0.7317 (mmm160) cc_final: 0.7036 (mmp-170) REVERT: D 90 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: G 64 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7414 (tp30) outliers start: 18 outliers final: 8 residues processed: 179 average time/residue: 1.8377 time to fit residues: 354.6150 Evaluate side-chains 176 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17205 Z= 0.179 Angle : 0.567 10.811 24484 Z= 0.327 Chirality : 0.035 0.149 2772 Planarity : 0.003 0.036 2097 Dihedral : 28.575 170.643 4627 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.37 % Allowed : 15.46 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.24), residues: 1274 helix: 2.21 (0.18), residues: 787 sheet: -0.15 (0.65), residues: 80 loop : -1.41 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 39 HIS 0.003 0.001 HIS L 75 PHE 0.021 0.001 PHE K 417 TYR 0.010 0.001 TYR K 214 ARG 0.008 0.000 ARG K 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: K 282 MET cc_start: 0.8414 (mmt) cc_final: 0.8163 (mmt) REVERT: C 92 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: G 64 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7407 (tp30) outliers start: 15 outliers final: 12 residues processed: 174 average time/residue: 1.9809 time to fit residues: 370.7483 Evaluate side-chains 182 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 17205 Z= 0.450 Angle : 0.666 10.533 24484 Z= 0.377 Chirality : 0.042 0.160 2772 Planarity : 0.004 0.051 2097 Dihedral : 28.918 160.993 4627 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.56 % Allowed : 15.37 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1274 helix: 1.84 (0.18), residues: 785 sheet: -0.24 (0.64), residues: 80 loop : -1.58 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 39 HIS 0.004 0.001 HIS L 75 PHE 0.028 0.002 PHE K 409 TYR 0.014 0.002 TYR F 51 ARG 0.007 0.001 ARG K 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: G 64 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7480 (tp30) outliers start: 17 outliers final: 10 residues processed: 177 average time/residue: 1.9585 time to fit residues: 373.0714 Evaluate side-chains 180 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17205 Z= 0.226 Angle : 0.626 11.709 24484 Z= 0.357 Chirality : 0.037 0.146 2772 Planarity : 0.004 0.044 2097 Dihedral : 28.913 155.771 4627 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 1.19 % Allowed : 16.29 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.24), residues: 1274 helix: 1.93 (0.18), residues: 785 sheet: -0.21 (0.65), residues: 80 loop : -1.51 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 39 HIS 0.004 0.001 HIS L 75 PHE 0.042 0.002 PHE K 409 TYR 0.013 0.001 TYR K 214 ARG 0.007 0.001 ARG K 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: G 64 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7452 (tp30) outliers start: 13 outliers final: 9 residues processed: 170 average time/residue: 2.0270 time to fit residues: 371.0657 Evaluate side-chains 174 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 5.9990 chunk 37 optimal weight: 0.0670 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.123610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.088305 restraints weight = 23490.647| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.49 r_work: 0.2990 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17205 Z= 0.227 Angle : 0.609 10.213 24484 Z= 0.348 Chirality : 0.037 0.140 2772 Planarity : 0.005 0.130 2097 Dihedral : 28.834 152.562 4627 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.91 % Allowed : 16.74 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1274 helix: 2.00 (0.18), residues: 785 sheet: -0.16 (0.64), residues: 80 loop : -1.41 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 39 HIS 0.003 0.001 HIS L 75 PHE 0.012 0.001 PHE K 417 TYR 0.012 0.001 TYR K 214 ARG 0.021 0.001 ARG K 614 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6271.49 seconds wall clock time: 113 minutes 11.74 seconds (6791.74 seconds total)