Starting phenix.real_space_refine on Mon Apr 8 04:07:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysu_34082/04_2024/7ysu_34082_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysu_34082/04_2024/7ysu_34082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysu_34082/04_2024/7ysu_34082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysu_34082/04_2024/7ysu_34082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysu_34082/04_2024/7ysu_34082_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysu_34082/04_2024/7ysu_34082_updated.pdb" } resolution = 3.2 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= 0.009 sd= 0.113 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 Cu 1 5.60 5 S 63 5.16 5 C 7923 2.51 5 N 2144 2.21 5 O 2298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 427": "OD1" <-> "OD2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 776": "OD1" <-> "OD2" Residue "A TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 162": "OD1" <-> "OD2" Residue "C PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "E TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 121": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12430 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 7527 Classifications: {'peptide': 921} Link IDs: {'PTRANS': 51, 'TRANS': 869} Chain breaks: 1 Chain: "C" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1645 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 196} Chain: "E" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1638 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 196} Chain: "B" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1442 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 16, 'TRANS': 162} Chain: "F" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 176 Unusual residues: {'IDS': 5, 'SGN': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5570 SG CYS A 739 44.317 45.769 99.144 1.00115.03 S Time building chain proxies: 6.52, per 1000 atoms: 0.52 Number of scatterers: 12430 At special positions: 0 Unit cell: (85.936, 121.568, 142.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 S 63 16.00 O 2298 8.00 N 2144 7.00 C 7923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 963 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 621 " distance=2.02 Simple disulfide: pdb=" SG CYS A 910 " - pdb=" SG CYS A 970 " distance=2.03 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 341 " distance=2.03 Simple disulfide: pdb=" SG CYS E 178 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS E 277 " - pdb=" SG CYS E 341 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 113 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Links applied ALPHA1-4 " IDS F 1 " - " SGN F 2 " " IDS F 3 " - " SGN F 4 " " IDS F 5 " - " SGN F 6 " " IDS F 7 " - " SGN F 8 " " IDS F 9 " - " SGN F 10 " BETA1-4 " SGN F 2 " - " IDS F 3 " ~> Even though IDS is an alpha isomer, a beta linkage is required... " SGN F 4 " - " IDS F 5 " " SGN F 6 " - " IDS F 7 " " SGN F 8 " - " IDS F 9 " Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.72 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 739 " 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 20 sheets defined 22.9% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 37 through 44 removed outlier: 4.275A pdb=" N GLN A 40 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TRP A 42 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 132 through 142 removed outlier: 3.758A pdb=" N THR A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 156 No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 167 through 183 removed outlier: 3.663A pdb=" N LEU A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 261 through 285 Processing helix chain 'A' and resid 287 through 290 No H-bonds generated for 'chain 'A' and resid 287 through 290' Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 325 through 332 Proline residue: A 330 - end of helix Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 382 through 385 No H-bonds generated for 'chain 'A' and resid 382 through 385' Processing helix chain 'A' and resid 394 through 404 Processing helix chain 'A' and resid 429 through 446 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 576 through 587 Proline residue: A 580 - end of helix Processing helix chain 'A' and resid 599 through 602 No H-bonds generated for 'chain 'A' and resid 599 through 602' Processing helix chain 'A' and resid 613 through 628 Processing helix chain 'A' and resid 649 through 652 No H-bonds generated for 'chain 'A' and resid 649 through 652' Processing helix chain 'A' and resid 660 through 676 Processing helix chain 'A' and resid 697 through 717 Processing helix chain 'A' and resid 744 through 756 Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 791 through 797 Processing helix chain 'A' and resid 849 through 862 removed outlier: 4.182A pdb=" N ARG A 853 " --> pdb=" O PRO A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 903 Processing helix chain 'A' and resid 939 through 949 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 166 through 170 Processing sheet with id= A, first strand: chain 'A' and resid 454 through 457 removed outlier: 6.282A pdb=" N LEU A 66 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA A 457 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA A 68 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS A 146 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN A 186 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE A 149 " --> pdb=" O GLN A 186 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 188 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR A 233 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN A 293 " --> pdb=" O TRP A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 302 through 304 Processing sheet with id= C, first strand: chain 'A' and resid 912 through 914 removed outlier: 6.274A pdb=" N HIS A 592 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 634 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 683 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS A 725 " --> pdb=" O TRP A 684 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 734 through 737 Processing sheet with id= E, first strand: chain 'A' and resid 804 through 806 Processing sheet with id= F, first strand: chain 'A' and resid 928 through 931 Processing sheet with id= G, first strand: chain 'A' and resid 367 through 372 removed outlier: 7.413A pdb=" N PHE A 371 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN A 415 " --> pdb=" O PHE A 371 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 165 through 169 removed outlier: 8.304A pdb=" N LEU C 166 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR C 244 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL C 168 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP C 246 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 174 through 177 Processing sheet with id= J, first strand: chain 'C' and resid 265 through 268 Processing sheet with id= K, first strand: chain 'C' and resid 273 through 276 Processing sheet with id= L, first strand: chain 'C' and resid 349 through 355 removed outlier: 4.507A pdb=" N GLU C 338 " --> pdb=" O HIS C 292 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS C 312 " --> pdb=" O TRP C 289 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS C 291 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL C 310 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 165 through 169 removed outlier: 8.694A pdb=" N LEU E 166 " --> pdb=" O THR E 242 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR E 244 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL E 168 " --> pdb=" O THR E 244 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP E 246 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER E 189 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU E 233 " --> pdb=" O SER E 187 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 174 through 177 Processing sheet with id= O, first strand: chain 'E' and resid 273 through 276 Processing sheet with id= P, first strand: chain 'E' and resid 286 through 288 Processing sheet with id= Q, first strand: chain 'B' and resid 158 through 161 removed outlier: 12.945A pdb=" N ILE B 40 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N ILE B 55 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU B 42 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 93 through 95 Processing sheet with id= S, first strand: chain 'B' and resid 115 through 119 Processing sheet with id= T, first strand: chain 'B' and resid 75 through 79 removed outlier: 6.903A pdb=" N PHE B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 867 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: 4.02 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3998 1.34 - 1.46: 3156 1.46 - 1.58: 5564 1.58 - 1.70: 6 1.70 - 1.82: 79 Bond restraints: 12803 Sorted by residual: bond pdb=" O2 IDS F 3 " pdb=" S IDS F 3 " ideal model delta sigma weight residual 1.646 1.526 0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" O2 IDS F 7 " pdb=" S IDS F 7 " ideal model delta sigma weight residual 1.646 1.527 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" O2 IDS F 1 " pdb=" S IDS F 1 " ideal model delta sigma weight residual 1.646 1.527 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" O2 IDS F 5 " pdb=" S IDS F 5 " ideal model delta sigma weight residual 1.646 1.527 0.119 2.00e-02 2.50e+03 3.51e+01 bond pdb=" O2 IDS F 9 " pdb=" S IDS F 9 " ideal model delta sigma weight residual 1.646 1.530 0.116 2.00e-02 2.50e+03 3.38e+01 ... (remaining 12798 not shown) Histogram of bond angle deviations from ideal: 90.95 - 101.02: 29 101.02 - 111.09: 5055 111.09 - 121.16: 8596 121.16 - 131.23: 3718 131.23 - 141.30: 53 Bond angle restraints: 17451 Sorted by residual: angle pdb=" C3 SGN F 6 " pdb=" C4 SGN F 6 " pdb=" O4 SGN F 6 " ideal model delta sigma weight residual 108.83 141.30 -32.47 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C5 IDS F 3 " pdb=" C4 IDS F 3 " pdb=" O4 IDS F 3 " ideal model delta sigma weight residual 113.47 140.07 -26.60 3.00e+00 1.11e-01 7.86e+01 angle pdb=" C3 IDS F 7 " pdb=" C4 IDS F 7 " pdb=" O4 IDS F 7 " ideal model delta sigma weight residual 108.24 133.74 -25.50 3.00e+00 1.11e-01 7.23e+01 angle pdb=" C5 SGN F 4 " pdb=" C4 SGN F 4 " pdb=" O4 SGN F 4 " ideal model delta sigma weight residual 108.84 129.30 -20.46 3.00e+00 1.11e-01 4.65e+01 angle pdb=" C5 SGN F 8 " pdb=" C4 SGN F 8 " pdb=" O4 SGN F 8 " ideal model delta sigma weight residual 108.84 129.22 -20.38 3.00e+00 1.11e-01 4.62e+01 ... (remaining 17446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 7271 34.45 - 68.91: 244 68.91 - 103.36: 55 103.36 - 137.81: 63 137.81 - 172.26: 14 Dihedral angle restraints: 7647 sinusoidal: 3235 harmonic: 4412 Sorted by residual: dihedral pdb=" CB CYS E 277 " pdb=" SG CYS E 277 " pdb=" SG CYS E 341 " pdb=" CB CYS E 341 " ideal model delta sinusoidal sigma weight residual 93.00 -177.71 -89.29 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CA HIS A 553 " pdb=" C HIS A 553 " pdb=" N SER A 554 " pdb=" CA SER A 554 " ideal model delta harmonic sigma weight residual 180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CB CYS B 95 " pdb=" SG CYS B 95 " pdb=" SG CYS B 113 " pdb=" CB CYS B 113 " ideal model delta sinusoidal sigma weight residual -86.00 -42.37 -43.63 1 1.00e+01 1.00e-02 2.65e+01 ... (remaining 7644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.966: 1848 0.966 - 1.933: 1 1.933 - 2.899: 1 2.899 - 3.866: 0 3.866 - 4.832: 4 Chirality restraints: 1854 Sorted by residual: chirality pdb=" C4 IDS F 5 " pdb=" C3 IDS F 5 " pdb=" C5 IDS F 5 " pdb=" O4 IDS F 5 " both_signs ideal model delta sigma weight residual False -2.41 2.42 -4.83 2.00e-01 2.50e+01 5.84e+02 chirality pdb=" C4 SGN F 4 " pdb=" C3 SGN F 4 " pdb=" C5 SGN F 4 " pdb=" O4 SGN F 4 " both_signs ideal model delta sigma weight residual False -2.48 2.01 -4.50 2.00e-01 2.50e+01 5.05e+02 chirality pdb=" C4 SGN F 8 " pdb=" C3 SGN F 8 " pdb=" C5 SGN F 8 " pdb=" O4 SGN F 8 " both_signs ideal model delta sigma weight residual False -2.48 1.88 -4.36 2.00e-01 2.50e+01 4.75e+02 ... (remaining 1851 not shown) Planarity restraints: 2233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 284 " 0.101 5.00e-02 4.00e+02 1.51e-01 3.66e+01 pdb=" N PRO E 285 " -0.261 5.00e-02 4.00e+02 pdb=" CA PRO E 285 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO E 285 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 64 " -0.073 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO B 65 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO B 65 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 65 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 219 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C TYR A 219 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR A 219 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 220 " 0.009 2.00e-02 2.50e+03 ... (remaining 2230 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 231 2.63 - 3.20: 10921 3.20 - 3.77: 19591 3.77 - 4.33: 26395 4.33 - 4.90: 44487 Nonbonded interactions: 101625 Sorted by model distance: nonbonded pdb=" OD1 ASP A 815 " pdb="ZN ZN A1001 " model vdw 2.065 2.230 nonbonded pdb=" OD1 ASP E 282 " pdb="CU CU E 401 " model vdw 2.078 2.240 nonbonded pdb=" OD1 ASP A 426 " pdb="ZN ZN A1001 " model vdw 2.089 2.230 nonbonded pdb=" O HIS B 168 " pdb=" OG1 THR B 171 " model vdw 2.133 2.440 nonbonded pdb=" OH TYR A 697 " pdb=" OH TYR A 827 " model vdw 2.147 2.440 ... (remaining 101620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and resid 150 through 359) selection = (chain 'E' and resid 150 through 359) } 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: 0.840 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: 4.110 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 37.700 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 : 0.005 0.120 12803 Z= 0.350 Angle : 0.940 32.473 17451 Z= 0.397 Chirality : 0.224 4.832 1854 Planarity : 0.005 0.151 2233 Dihedral : 23.912 172.262 4795 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.31 % Allowed : 22.28 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.21), residues: 1511 helix: 0.44 (0.29), residues: 366 sheet: -1.53 (0.30), residues: 301 loop : -2.23 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 90 HIS 0.004 0.001 HIS E 286 PHE 0.011 0.001 PHE A 352 TYR 0.014 0.001 TYR A 890 ARG 0.003 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 1.403 Fit side-chains REVERT: A 772 TRP cc_start: 0.7973 (t-100) cc_final: 0.7370 (t-100) REVERT: E 201 HIS cc_start: 0.7205 (m-70) cc_final: 0.6893 (m90) REVERT: E 286 HIS cc_start: 0.8023 (t-90) cc_final: 0.7676 (t70) REVERT: B 89 MET cc_start: 0.8215 (mmm) cc_final: 0.7898 (tpt) outliers start: 4 outliers final: 1 residues processed: 112 average time/residue: 0.2448 time to fit residues: 41.1940 Evaluate side-chains 108 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN A 873 ASN C 201 HIS ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.0454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12803 Z= 0.226 Angle : 0.658 12.524 17451 Z= 0.304 Chirality : 0.048 0.448 1854 Planarity : 0.004 0.101 2233 Dihedral : 23.245 128.516 1910 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.60 % Allowed : 21.90 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.96 (0.21), residues: 1511 helix: 0.51 (0.28), residues: 378 sheet: -1.55 (0.29), residues: 319 loop : -2.14 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 466 HIS 0.004 0.001 HIS B 117 PHE 0.013 0.001 PHE A 595 TYR 0.013 0.001 TYR A 241 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 119 time to evaluate : 1.430 Fit side-chains REVERT: A 384 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7135 (mmm) REVERT: A 772 TRP cc_start: 0.8077 (t-100) cc_final: 0.7588 (t-100) REVERT: A 804 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7573 (tt) REVERT: C 162 ASP cc_start: 0.8144 (m-30) cc_final: 0.7852 (m-30) REVERT: E 201 HIS cc_start: 0.7146 (m-70) cc_final: 0.6922 (m90) outliers start: 34 outliers final: 13 residues processed: 149 average time/residue: 0.2221 time to fit residues: 50.8539 Evaluate side-chains 129 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 96 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 122 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 110 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN A 873 ASN C 201 HIS ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.0602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12803 Z= 0.200 Angle : 0.595 8.521 17451 Z= 0.286 Chirality : 0.047 0.426 1854 Planarity : 0.004 0.081 2233 Dihedral : 21.112 121.105 1908 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.37 % Allowed : 21.29 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.85 (0.21), residues: 1511 helix: 0.69 (0.28), residues: 378 sheet: -1.48 (0.29), residues: 328 loop : -2.12 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 466 HIS 0.004 0.001 HIS B 117 PHE 0.012 0.001 PHE A 595 TYR 0.020 0.001 TYR E 243 ARG 0.002 0.000 ARG E 240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 119 time to evaluate : 1.418 Fit side-chains REVERT: A 384 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7144 (mmm) REVERT: A 651 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6632 (mm) REVERT: A 772 TRP cc_start: 0.8018 (t-100) cc_final: 0.7538 (t-100) REVERT: A 804 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7610 (tt) REVERT: C 162 ASP cc_start: 0.8138 (m-30) cc_final: 0.7853 (m-30) REVERT: C 286 HIS cc_start: 0.8693 (OUTLIER) cc_final: 0.7655 (t70) REVERT: E 190 TRP cc_start: 0.7198 (m100) cc_final: 0.6952 (m100) REVERT: E 201 HIS cc_start: 0.7055 (m-70) cc_final: 0.6819 (m90) REVERT: B 25 TYR cc_start: 0.0868 (OUTLIER) cc_final: -0.1003 (t80) REVERT: B 89 MET cc_start: 0.8132 (tpt) cc_final: 0.7318 (tpt) REVERT: B 109 ASP cc_start: 0.7685 (t0) cc_final: 0.7451 (t0) outliers start: 44 outliers final: 25 residues processed: 152 average time/residue: 0.2294 time to fit residues: 52.8433 Evaluate side-chains 147 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain E residue 286 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 351 HIS Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 121 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 0.2980 chunk 39 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN C 201 HIS ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12803 Z= 0.155 Angle : 0.570 8.821 17451 Z= 0.273 Chirality : 0.045 0.367 1854 Planarity : 0.004 0.067 2233 Dihedral : 19.264 117.381 1908 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.75 % Allowed : 21.13 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.67 (0.22), residues: 1511 helix: 0.95 (0.28), residues: 371 sheet: -1.30 (0.30), residues: 313 loop : -2.07 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 466 HIS 0.004 0.001 HIS E 286 PHE 0.010 0.001 PHE A 925 TYR 0.008 0.001 TYR A 669 ARG 0.002 0.000 ARG E 240 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 123 time to evaluate : 1.559 Fit side-chains REVERT: A 324 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7345 (tp) REVERT: A 384 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7173 (mmm) REVERT: A 651 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6588 (mm) REVERT: A 772 TRP cc_start: 0.7956 (t-100) cc_final: 0.7527 (t-100) REVERT: C 161 MET cc_start: 0.7298 (ttm) cc_final: 0.6510 (mtp) REVERT: C 162 ASP cc_start: 0.8173 (m-30) cc_final: 0.7916 (m-30) REVERT: C 241 GLN cc_start: 0.7453 (tp-100) cc_final: 0.6044 (tt0) REVERT: E 190 TRP cc_start: 0.7221 (m100) cc_final: 0.6970 (m100) REVERT: E 201 HIS cc_start: 0.7069 (m-70) cc_final: 0.6815 (m90) REVERT: E 243 TYR cc_start: 0.8394 (m-80) cc_final: 0.7956 (m-80) REVERT: B 25 TYR cc_start: 0.0731 (OUTLIER) cc_final: -0.1095 (t80) REVERT: B 49 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7448 (t0) REVERT: B 89 MET cc_start: 0.8124 (tpt) cc_final: 0.7256 (tpt) REVERT: B 109 ASP cc_start: 0.7595 (t0) cc_final: 0.7304 (t0) outliers start: 49 outliers final: 28 residues processed: 162 average time/residue: 0.2249 time to fit residues: 55.3932 Evaluate side-chains 149 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 970 CYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 286 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 351 HIS Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 101 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 131 optimal weight: 30.0000 chunk 36 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN A 873 ASN C 201 HIS C 288 GLN ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12803 Z= 0.408 Angle : 0.675 8.859 17451 Z= 0.331 Chirality : 0.050 0.356 1854 Planarity : 0.004 0.061 2233 Dihedral : 18.344 116.160 1908 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.75 % Allowed : 21.52 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.86 (0.21), residues: 1511 helix: 0.55 (0.28), residues: 378 sheet: -1.46 (0.29), residues: 319 loop : -2.06 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 466 HIS 0.009 0.001 HIS B 117 PHE 0.022 0.002 PHE A 595 TYR 0.021 0.002 TYR A 669 ARG 0.003 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 118 time to evaluate : 1.431 Fit side-chains REVERT: A 148 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.5749 (tmt170) REVERT: A 384 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7169 (mmm) REVERT: A 651 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6690 (mm) REVERT: A 772 TRP cc_start: 0.8120 (t-100) cc_final: 0.7767 (t-100) REVERT: A 804 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7575 (tt) REVERT: A 936 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 162 ASP cc_start: 0.8184 (m-30) cc_final: 0.7941 (m-30) REVERT: C 241 GLN cc_start: 0.7503 (tp-100) cc_final: 0.7111 (tp-100) REVERT: C 286 HIS cc_start: 0.8712 (OUTLIER) cc_final: 0.7670 (t70) REVERT: E 190 TRP cc_start: 0.7187 (m100) cc_final: 0.6908 (m100) REVERT: E 201 HIS cc_start: 0.6960 (m-70) cc_final: 0.6700 (m90) REVERT: B 25 TYR cc_start: 0.1247 (OUTLIER) cc_final: -0.0739 (t80) REVERT: B 49 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7308 (t0) REVERT: B 89 MET cc_start: 0.8171 (tpt) cc_final: 0.7326 (tpt) REVERT: B 109 ASP cc_start: 0.7841 (t0) cc_final: 0.7579 (t0) outliers start: 62 outliers final: 36 residues processed: 168 average time/residue: 0.2221 time to fit residues: 57.0635 Evaluate side-chains 158 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 115 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 351 HIS Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 101 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.0040 chunk 131 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 146 optimal weight: 0.4980 chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN A 873 ASN C 201 HIS ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12803 Z= 0.166 Angle : 0.592 9.085 17451 Z= 0.282 Chirality : 0.045 0.306 1854 Planarity : 0.004 0.056 2233 Dihedral : 17.176 118.733 1908 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.06 % Allowed : 22.89 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.63 (0.22), residues: 1511 helix: 0.76 (0.28), residues: 383 sheet: -1.28 (0.30), residues: 313 loop : -1.97 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 466 HIS 0.003 0.001 HIS E 286 PHE 0.011 0.001 PHE A 418 TYR 0.020 0.001 TYR E 243 ARG 0.001 0.000 ARG C 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 117 time to evaluate : 1.549 Fit side-chains REVERT: A 384 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7176 (mmm) REVERT: A 651 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6590 (mm) REVERT: A 772 TRP cc_start: 0.7978 (t-100) cc_final: 0.7518 (t-100) REVERT: A 804 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7663 (tt) REVERT: C 162 ASP cc_start: 0.8227 (m-30) cc_final: 0.7994 (m-30) REVERT: C 241 GLN cc_start: 0.7184 (tp-100) cc_final: 0.6857 (tp-100) REVERT: E 190 TRP cc_start: 0.7158 (m100) cc_final: 0.6934 (m100) REVERT: E 201 HIS cc_start: 0.6999 (m-70) cc_final: 0.6727 (m90) REVERT: E 243 TYR cc_start: 0.8359 (m-80) cc_final: 0.7945 (m-80) REVERT: B 25 TYR cc_start: 0.1250 (OUTLIER) cc_final: -0.0722 (t80) REVERT: B 49 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7453 (t0) REVERT: B 109 ASP cc_start: 0.7714 (t0) cc_final: 0.7463 (t0) outliers start: 40 outliers final: 29 residues processed: 147 average time/residue: 0.2324 time to fit residues: 52.3343 Evaluate side-chains 150 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 116 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 286 HIS Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 351 HIS Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 79 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN C 201 HIS ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12803 Z= 0.280 Angle : 0.615 8.939 17451 Z= 0.296 Chirality : 0.046 0.284 1854 Planarity : 0.004 0.080 2233 Dihedral : 16.515 117.996 1908 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.83 % Allowed : 22.59 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.66 (0.22), residues: 1511 helix: 0.79 (0.28), residues: 377 sheet: -1.36 (0.29), residues: 323 loop : -1.96 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 466 HIS 0.006 0.001 HIS B 117 PHE 0.017 0.001 PHE A 595 TYR 0.018 0.001 TYR E 243 ARG 0.002 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 116 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 384 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7185 (mmm) REVERT: A 651 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6664 (mm) REVERT: A 772 TRP cc_start: 0.8020 (t-100) cc_final: 0.7634 (t-100) REVERT: A 804 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7621 (tt) REVERT: C 162 ASP cc_start: 0.8224 (m-30) cc_final: 0.7998 (m-30) REVERT: C 241 GLN cc_start: 0.7330 (tp-100) cc_final: 0.6908 (tp-100) REVERT: E 190 TRP cc_start: 0.7164 (m100) cc_final: 0.6891 (m100) REVERT: E 201 HIS cc_start: 0.6965 (m-70) cc_final: 0.6686 (m90) REVERT: E 243 TYR cc_start: 0.8371 (m-80) cc_final: 0.7880 (m-80) REVERT: B 25 TYR cc_start: 0.1126 (OUTLIER) cc_final: -0.0775 (t80) REVERT: B 49 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7279 (t0) REVERT: B 109 ASP cc_start: 0.7753 (t0) cc_final: 0.7489 (t0) outliers start: 50 outliers final: 39 residues processed: 154 average time/residue: 0.2363 time to fit residues: 55.8857 Evaluate side-chains 159 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 115 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 351 HIS Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 125 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 92 optimal weight: 0.0010 chunk 99 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN C 201 HIS ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12803 Z= 0.157 Angle : 0.576 8.930 17451 Z= 0.275 Chirality : 0.044 0.256 1854 Planarity : 0.004 0.071 2233 Dihedral : 15.775 116.222 1908 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.14 % Allowed : 23.43 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.47 (0.22), residues: 1511 helix: 1.08 (0.29), residues: 371 sheet: -1.21 (0.30), residues: 314 loop : -1.91 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 466 HIS 0.004 0.001 HIS E 286 PHE 0.010 0.001 PHE A 925 TYR 0.016 0.001 TYR E 243 ARG 0.002 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 118 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: A 384 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7210 (mmm) REVERT: A 461 MET cc_start: 0.8299 (ptp) cc_final: 0.8095 (ptp) REVERT: A 651 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6588 (mm) REVERT: A 688 ASN cc_start: 0.8004 (t0) cc_final: 0.7605 (p0) REVERT: A 772 TRP cc_start: 0.7954 (t-100) cc_final: 0.7498 (t-100) REVERT: A 804 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7605 (tt) REVERT: C 162 ASP cc_start: 0.8235 (m-30) cc_final: 0.8030 (m-30) REVERT: E 201 HIS cc_start: 0.7119 (m-70) cc_final: 0.6815 (m90) REVERT: E 243 TYR cc_start: 0.8379 (m-80) cc_final: 0.7933 (m-80) REVERT: B 25 TYR cc_start: 0.1068 (OUTLIER) cc_final: -0.0868 (t80) REVERT: B 49 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7354 (t0) REVERT: B 89 MET cc_start: 0.8210 (tpp) cc_final: 0.7955 (mmt) REVERT: B 109 ASP cc_start: 0.7668 (t0) cc_final: 0.7411 (t0) outliers start: 41 outliers final: 32 residues processed: 151 average time/residue: 0.2313 time to fit residues: 53.0063 Evaluate side-chains 151 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 351 HIS Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 125 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 3.9990 chunk 127 optimal weight: 0.0040 chunk 135 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN C 201 HIS ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12803 Z= 0.295 Angle : 0.621 8.291 17451 Z= 0.301 Chirality : 0.047 0.253 1854 Planarity : 0.004 0.073 2233 Dihedral : 15.444 114.405 1908 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.83 % Allowed : 23.20 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.58 (0.22), residues: 1511 helix: 0.80 (0.28), residues: 378 sheet: -1.16 (0.30), residues: 315 loop : -1.96 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 466 HIS 0.006 0.001 HIS B 117 PHE 0.017 0.001 PHE A 595 TYR 0.017 0.001 TYR E 243 ARG 0.002 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 115 time to evaluate : 1.453 Fit side-chains revert: symmetry clash REVERT: A 384 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7205 (mmm) REVERT: A 651 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6666 (mm) REVERT: A 804 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7625 (tt) REVERT: C 162 ASP cc_start: 0.8162 (m-30) cc_final: 0.7943 (m-30) REVERT: C 286 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.7590 (t70) REVERT: E 190 TRP cc_start: 0.7301 (m100) cc_final: 0.7033 (m100) REVERT: E 201 HIS cc_start: 0.7014 (m-70) cc_final: 0.6700 (m90) REVERT: E 243 TYR cc_start: 0.8419 (m-80) cc_final: 0.7895 (m-80) REVERT: B 25 TYR cc_start: 0.1176 (OUTLIER) cc_final: -0.0858 (t80) REVERT: B 49 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7263 (t0) REVERT: B 109 ASP cc_start: 0.7740 (t0) cc_final: 0.7460 (t0) outliers start: 50 outliers final: 42 residues processed: 154 average time/residue: 0.2193 time to fit residues: 51.9661 Evaluate side-chains 162 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 114 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 286 HIS Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 351 HIS Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 125 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 3.9990 chunk 68 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 150 optimal weight: 0.4980 chunk 138 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 92 optimal weight: 0.0010 chunk 73 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN C 201 HIS ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12803 Z= 0.159 Angle : 0.578 8.801 17451 Z= 0.277 Chirality : 0.045 0.286 1854 Planarity : 0.004 0.069 2233 Dihedral : 14.858 112.951 1908 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.45 % Allowed : 23.58 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.42 (0.22), residues: 1511 helix: 1.13 (0.29), residues: 371 sheet: -1.12 (0.29), residues: 330 loop : -1.93 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 466 HIS 0.006 0.001 HIS E 286 PHE 0.011 0.001 PHE A 925 TYR 0.017 0.001 TYR E 243 ARG 0.002 0.000 ARG B 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3022 Ramachandran restraints generated. 1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 118 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 384 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7231 (mmm) REVERT: A 461 MET cc_start: 0.8306 (ptp) cc_final: 0.8084 (ptp) REVERT: A 651 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6614 (mm) REVERT: A 688 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7716 (p0) REVERT: A 772 TRP cc_start: 0.7980 (t-100) cc_final: 0.7584 (t-100) REVERT: A 804 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7578 (tt) REVERT: C 281 SER cc_start: 0.7126 (t) cc_final: 0.6653 (p) REVERT: E 201 HIS cc_start: 0.7137 (m-70) cc_final: 0.6832 (m90) REVERT: E 243 TYR cc_start: 0.8397 (m-80) cc_final: 0.7976 (m-80) REVERT: B 25 TYR cc_start: 0.1173 (OUTLIER) cc_final: -0.0831 (t80) REVERT: B 49 ASN cc_start: 0.7764 (OUTLIER) cc_final: 0.7232 (t0) REVERT: B 68 THR cc_start: 0.8184 (p) cc_final: 0.7967 (p) REVERT: B 109 ASP cc_start: 0.7648 (t0) cc_final: 0.7404 (t0) outliers start: 45 outliers final: 36 residues processed: 154 average time/residue: 0.2394 time to fit residues: 56.6224 Evaluate side-chains 157 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 115 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 286 HIS Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 351 HIS Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 125 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN C 201 HIS ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.141669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.092566 restraints weight = 17701.315| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.10 r_work: 0.3161 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12803 Z= 0.266 Angle : 0.608 8.844 17451 Z= 0.294 Chirality : 0.046 0.309 1854 Planarity : 0.004 0.072 2233 Dihedral : 14.547 111.807 1908 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.52 % Allowed : 23.51 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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 (0.22), residues: 1511 helix: 1.00 (0.29), residues: 372 sheet: -1.19 (0.30), residues: 325 loop : -1.85 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 466 HIS 0.005 0.001 HIS B 117 PHE 0.016 0.001 PHE A 595 TYR 0.016 0.001 TYR E 243 ARG 0.002 0.000 ARG C 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2672.18 seconds wall clock time: 52 minutes 20.41 seconds (3140.41 seconds total)