Starting phenix.real_space_refine on Mon Mar 11 18:28:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k65_22689/03_2024/7k65_22689_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k65_22689/03_2024/7k65_22689.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k65_22689/03_2024/7k65_22689_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k65_22689/03_2024/7k65_22689_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k65_22689/03_2024/7k65_22689_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k65_22689/03_2024/7k65_22689.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k65_22689/03_2024/7k65_22689.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k65_22689/03_2024/7k65_22689_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k65_22689/03_2024/7k65_22689_updated.pdb" } resolution = 3.4 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= -0.021 sd= 0.878 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5734 2.51 5 N 1415 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 246": "OD1" <-> "OD2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 765": "OD1" <-> "OD2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A TYR 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 865": "OD1" <-> "OD2" Residue "A ASP 895": "OD1" <-> "OD2" Residue "A TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 940": "OD1" <-> "OD2" Residue "A TYR 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 953": "OE1" <-> "OE2" Residue "A PHE 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 975": "OE1" <-> "OE2" Residue "A GLU 978": "OE1" <-> "OE2" Residue "A TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1052": "OE1" <-> "OE2" Residue "A PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1132": "OD1" <-> "OD2" Residue "A PHE 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 61": "OD1" <-> "OD2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8796 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7666 Classifications: {'peptide': 1005} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 959} Chain breaks: 1 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 166 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 858 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 244 Unusual residues: {'NAG': 5, 'Q7G': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 65 Time building chain proxies: 4.96, per 1000 atoms: 0.56 Number of scatterers: 8796 At special positions: 0 Unit cell: (122.844, 121.785, 95.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1600 8.00 N 1415 7.00 C 5734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 313 " distance=2.34 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 290 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " 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=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1401 " - " ASN A 400 " " NAG A1402 " - " ASN A 127 " " NAG A1403 " - " ASN A 298 " " NAG A1404 " - " ASN A 861 " " NAG A1405 " - " ASN A 335 " " NAG C 1 " - " ASN A 986 " Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.9 seconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 6 sheets defined 52.7% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 61 through 82 Processing helix chain 'A' and resid 86 through 103 removed outlier: 3.918A pdb=" N GLY A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 114 No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 202 through 209 removed outlier: 3.541A pdb=" N TYR A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 247 through 257 removed outlier: 3.722A pdb=" N ILE A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 375 through 396 Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 425 through 443 Processing helix chain 'A' and resid 452 through 477 removed outlier: 4.872A pdb=" N LEU A 457 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 489 through 512 removed outlier: 3.966A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 549 removed outlier: 5.924A pdb=" N THR A 523 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLY A 531 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA A 532 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA A 535 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A 538 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE A 539 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 576 Processing helix chain 'A' and resid 578 through 589 Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 727 through 731 Processing helix chain 'A' and resid 733 through 753 Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 802 through 814 removed outlier: 3.836A pdb=" N PHE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER A 813 " --> pdb=" O HIS A 809 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN A 814 " --> pdb=" O LYS A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 850 Processing helix chain 'A' and resid 864 through 873 Processing helix chain 'A' and resid 886 through 889 Processing helix chain 'A' and resid 905 through 915 Processing helix chain 'A' and resid 917 through 923 Processing helix chain 'A' and resid 943 through 946 No H-bonds generated for 'chain 'A' and resid 943 through 946' Processing helix chain 'A' and resid 971 through 988 Processing helix chain 'A' and resid 999 through 1001 No H-bonds generated for 'chain 'A' and resid 999 through 1001' Processing helix chain 'A' and resid 1006 through 1008 No H-bonds generated for 'chain 'A' and resid 1006 through 1008' Processing helix chain 'A' and resid 1010 through 1033 Processing helix chain 'A' and resid 1036 through 1060 Processing helix chain 'A' and resid 1066 through 1081 removed outlier: 4.708A pdb=" N VAL A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1091 Processing helix chain 'A' and resid 1097 through 1128 removed outlier: 5.435A pdb=" N ALA A1110 " --> pdb=" O GLU A1106 " (cutoff:3.500A) Proline residue: A1111 - end of helix removed outlier: 4.253A pdb=" N MET A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A1127 " --> pdb=" O VAL A1123 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY A1128 " --> pdb=" O LEU A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1137 Processing helix chain 'A' and resid 1139 through 1153 Processing helix chain 'A' and resid 1156 through 1163 Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing sheet with id= A, first strand: chain 'A' and resid 346 through 352 Processing sheet with id= B, first strand: chain 'A' and resid 175 through 178 Processing sheet with id= C, first strand: chain 'A' and resid 957 through 964 Processing sheet with id= D, first strand: chain 'A' and resid 332 through 334 Processing sheet with id= E, first strand: chain 'B' and resid 5 through 7 Processing sheet with id= F, first strand: chain 'B' and resid 112 through 114 removed outlier: 5.177A pdb=" N ARG B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 3.71 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: 2716 1.34 - 1.46: 2196 1.46 - 1.58: 4039 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9027 Sorted by residual: bond pdb=" C04 Q7G A1406 " pdb=" C05 Q7G A1406 " ideal model delta sigma weight residual 1.836 1.524 0.312 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C04 Q7G A1407 " pdb=" C05 Q7G A1407 " ideal model delta sigma weight residual 1.836 1.541 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C04 Q7G A1409 " pdb=" C05 Q7G A1409 " ideal model delta sigma weight residual 1.836 1.542 0.294 2.00e-02 2.50e+03 2.16e+02 bond pdb=" C04 Q7G A1408 " pdb=" C05 Q7G A1408 " ideal model delta sigma weight residual 1.836 1.545 0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C07 Q7G A1406 " pdb=" C15 Q7G A1406 " ideal model delta sigma weight residual 1.779 1.500 0.279 2.00e-02 2.50e+03 1.95e+02 ... (remaining 9022 not shown) Histogram of bond angle deviations from ideal: 95.14 - 102.93: 83 102.93 - 110.71: 3100 110.71 - 118.50: 4079 118.50 - 126.28: 4959 126.28 - 134.06: 147 Bond angle restraints: 12368 Sorted by residual: angle pdb=" C LYS A 334 " pdb=" N ASN A 335 " pdb=" CA ASN A 335 " ideal model delta sigma weight residual 122.40 127.45 -5.05 1.45e+00 4.76e-01 1.22e+01 angle pdb=" C11 Q7G A1407 " pdb=" C13 Q7G A1407 " pdb=" C16 Q7G A1407 " ideal model delta sigma weight residual 111.23 121.66 -10.43 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C11 Q7G A1408 " pdb=" C13 Q7G A1408 " pdb=" C16 Q7G A1408 " ideal model delta sigma weight residual 111.23 121.65 -10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C ILE A 949 " pdb=" CA ILE A 949 " pdb=" CB ILE A 949 " ideal model delta sigma weight residual 111.00 114.37 -3.37 9.80e-01 1.04e+00 1.18e+01 angle pdb=" C11 Q7G A1409 " pdb=" C13 Q7G A1409 " pdb=" C16 Q7G A1409 " ideal model delta sigma weight residual 111.23 121.47 -10.24 3.00e+00 1.11e-01 1.17e+01 ... (remaining 12363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.09: 5086 23.09 - 46.18: 254 46.18 - 69.27: 28 69.27 - 92.36: 15 92.36 - 115.45: 10 Dihedral angle restraints: 5393 sinusoidal: 2138 harmonic: 3255 Sorted by residual: dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 313 " pdb=" CB CYS A 313 " ideal model delta sinusoidal sigma weight residual -86.00 0.84 -86.84 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CA ASN A 335 " pdb=" C ASN A 335 " pdb=" N ALA A 336 " pdb=" CA ALA A 336 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C1C Q7G A1406 " pdb=" C48 Q7G A1406 " pdb=" O1C Q7G A1406 " pdb=" C23 Q7G A1406 " ideal model delta sinusoidal sigma weight residual -159.04 -43.59 -115.45 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 5390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 1454 0.136 - 0.273: 14 0.273 - 0.409: 0 0.409 - 0.545: 5 0.545 - 0.681: 8 Chirality restraints: 1481 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-02 2.50e+03 5.81e+02 chirality pdb=" C11 Q7G A1406 " pdb=" C08 Q7G A1406 " pdb=" C13 Q7G A1406 " pdb=" C19 Q7G A1406 " both_signs ideal model delta sigma weight residual False 3.01 2.33 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C11 Q7G A1408 " pdb=" C08 Q7G A1408 " pdb=" C13 Q7G A1408 " pdb=" C19 Q7G A1408 " both_signs ideal model delta sigma weight residual False 3.01 2.36 0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 1478 not shown) Planarity restraints: 1527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 Q7G A1406 " -0.013 2.00e-02 2.50e+03 1.88e-02 4.41e+00 pdb=" C13 Q7G A1406 " 0.030 2.00e-02 2.50e+03 pdb=" C14 Q7G A1406 " -0.025 2.00e-02 2.50e+03 pdb=" C15 Q7G A1406 " 0.011 2.00e-02 2.50e+03 pdb=" C16 Q7G A1406 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 Q7G A1409 " 0.012 2.00e-02 2.50e+03 1.80e-02 4.04e+00 pdb=" C13 Q7G A1409 " -0.029 2.00e-02 2.50e+03 pdb=" C14 Q7G A1409 " 0.023 2.00e-02 2.50e+03 pdb=" C15 Q7G A1409 " -0.009 2.00e-02 2.50e+03 pdb=" C16 Q7G A1409 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 Q7G A1407 " 0.012 2.00e-02 2.50e+03 1.79e-02 4.00e+00 pdb=" C13 Q7G A1407 " -0.029 2.00e-02 2.50e+03 pdb=" C14 Q7G A1407 " 0.023 2.00e-02 2.50e+03 pdb=" C15 Q7G A1407 " -0.010 2.00e-02 2.50e+03 pdb=" C16 Q7G A1407 " 0.003 2.00e-02 2.50e+03 ... (remaining 1524 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1185 2.75 - 3.29: 9098 3.29 - 3.83: 14987 3.83 - 4.36: 16771 4.36 - 4.90: 28673 Nonbonded interactions: 70714 Sorted by model distance: nonbonded pdb=" O PRO A 929 " pdb=" NH1 ARG A 931 " model vdw 2.213 2.520 nonbonded pdb=" NE2 GLN A 875 " pdb=" O LEU A 947 " model vdw 2.225 2.520 nonbonded pdb=" O MET A 278 " pdb=" OG1 THR A 293 " model vdw 2.226 2.440 nonbonded pdb=" O ASP A1096 " pdb=" N ARG A1100 " model vdw 2.253 2.520 nonbonded pdb=" O LYS A 810 " pdb=" OG SER A 813 " model vdw 2.256 2.440 ... (remaining 70709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.220 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 27.810 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.016 0.312 9027 Z= 1.035 Angle : 0.859 10.428 12368 Z= 0.413 Chirality : 0.070 0.681 1481 Planarity : 0.004 0.037 1521 Dihedral : 14.990 115.447 3293 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.91 (0.24), residues: 1114 helix: -0.78 (0.19), residues: 566 sheet: -1.34 (0.51), residues: 99 loop : -1.75 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 830 HIS 0.003 0.001 HIS A 187 PHE 0.015 0.001 PHE A 743 TYR 0.010 0.001 TYR A 995 ARG 0.003 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 131 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8450 (mt0) REVERT: A 181 ARG cc_start: 0.8106 (mmt-90) cc_final: 0.7903 (mmm160) REVERT: A 220 CYS cc_start: 0.6628 (p) cc_final: 0.6154 (p) REVERT: A 278 MET cc_start: 0.9002 (mmp) cc_final: 0.8718 (mmm) REVERT: A 284 ASN cc_start: 0.8992 (m110) cc_final: 0.8727 (m110) REVERT: A 301 LYS cc_start: 0.9270 (pttt) cc_final: 0.9032 (ptpp) REVERT: A 325 GLU cc_start: 0.8323 (pm20) cc_final: 0.8115 (pm20) REVERT: A 351 GLN cc_start: 0.8188 (mt0) cc_final: 0.7857 (mt0) REVERT: A 443 MET cc_start: 0.7941 (mmp) cc_final: 0.7425 (mmm) REVERT: A 892 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7979 (mmm160) REVERT: A 949 ILE cc_start: 0.8757 (tt) cc_final: 0.8183 (tt) REVERT: A 969 ASP cc_start: 0.7753 (t0) cc_final: 0.7299 (t0) REVERT: A 972 ASP cc_start: 0.8255 (m-30) cc_final: 0.8046 (m-30) REVERT: A 975 GLU cc_start: 0.8419 (tp30) cc_final: 0.8105 (tp30) REVERT: A 1035 ASN cc_start: 0.8100 (t0) cc_final: 0.7780 (t0) REVERT: A 1102 MET cc_start: 0.9049 (mtt) cc_final: 0.8600 (mtm) REVERT: A 1136 ARG cc_start: 0.8615 (mtp180) cc_final: 0.8012 (ttm-80) REVERT: A 1163 PHE cc_start: 0.7534 (m-80) cc_final: 0.7328 (m-10) REVERT: A 1164 PHE cc_start: 0.6847 (t80) cc_final: 0.6063 (t80) REVERT: B 29 PHE cc_start: 0.8601 (t80) cc_final: 0.8391 (t80) REVERT: B 82 MET cc_start: 0.7056 (mtt) cc_final: 0.6735 (tmm) REVERT: B 104 TYR cc_start: 0.9045 (p90) cc_final: 0.8319 (p90) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2078 time to fit residues: 74.2467 Evaluate side-chains 194 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 258 ASN A 513 GLN ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 HIS A1152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9027 Z= 0.218 Angle : 0.613 8.718 12368 Z= 0.292 Chirality : 0.043 0.286 1481 Planarity : 0.004 0.037 1521 Dihedral : 10.790 122.164 1482 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.11 % Allowed : 15.32 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.26), residues: 1114 helix: 0.48 (0.22), residues: 565 sheet: -0.90 (0.52), residues: 97 loop : -1.31 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1037 HIS 0.010 0.001 HIS A 936 PHE 0.015 0.001 PHE A1164 TYR 0.012 0.001 TYR B 59 ARG 0.003 0.000 ARG A 948 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 131 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8337 (mm110) REVERT: A 265 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8134 (mt-10) REVERT: A 284 ASN cc_start: 0.9006 (m110) cc_final: 0.8745 (m110) REVERT: A 301 LYS cc_start: 0.9276 (pttt) cc_final: 0.9039 (ptpp) REVERT: A 351 GLN cc_start: 0.8228 (mt0) cc_final: 0.7904 (mt0) REVERT: A 569 PHE cc_start: 0.8501 (m-10) cc_final: 0.8198 (m-10) REVERT: A 969 ASP cc_start: 0.7711 (t0) cc_final: 0.7205 (t0) REVERT: A 972 ASP cc_start: 0.8249 (m-30) cc_final: 0.8027 (m-30) REVERT: A 975 GLU cc_start: 0.8493 (tp30) cc_final: 0.8109 (tp30) REVERT: A 999 TYR cc_start: 0.8318 (m-10) cc_final: 0.7501 (m-80) REVERT: A 1035 ASN cc_start: 0.8188 (t0) cc_final: 0.7825 (t0) REVERT: A 1102 MET cc_start: 0.8948 (mtt) cc_final: 0.8528 (mtm) REVERT: A 1136 ARG cc_start: 0.8528 (mtp180) cc_final: 0.7786 (ttm110) REVERT: B 104 TYR cc_start: 0.9186 (p90) cc_final: 0.8323 (p90) outliers start: 27 outliers final: 19 residues processed: 215 average time/residue: 0.1935 time to fit residues: 58.8513 Evaluate side-chains 203 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 810 LYS Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1117 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 0.0570 chunk 100 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS A1152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9027 Z= 0.173 Angle : 0.575 7.608 12368 Z= 0.277 Chirality : 0.041 0.244 1481 Planarity : 0.004 0.035 1521 Dihedral : 10.466 121.763 1482 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.23 % Allowed : 18.78 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.17 (0.26), residues: 1114 helix: 0.88 (0.22), residues: 564 sheet: -0.70 (0.52), residues: 93 loop : -1.21 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.007 0.001 HIS A 936 PHE 0.020 0.001 PHE A1032 TYR 0.009 0.001 TYR A 995 ARG 0.003 0.000 ARG A 948 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 0.999 Fit side-chains REVERT: A 265 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8003 (mt-10) REVERT: A 284 ASN cc_start: 0.9001 (m110) cc_final: 0.8746 (m110) REVERT: A 301 LYS cc_start: 0.9244 (pttt) cc_final: 0.9000 (ptpp) REVERT: A 351 GLN cc_start: 0.8241 (mt0) cc_final: 0.7877 (mt0) REVERT: A 569 PHE cc_start: 0.8499 (m-10) cc_final: 0.8215 (m-10) REVERT: A 892 ARG cc_start: 0.8240 (mmm-85) cc_final: 0.7690 (mmm160) REVERT: A 969 ASP cc_start: 0.7684 (t0) cc_final: 0.7213 (t0) REVERT: A 975 GLU cc_start: 0.8465 (tp30) cc_final: 0.7954 (tp30) REVERT: A 999 TYR cc_start: 0.8338 (m-10) cc_final: 0.7507 (m-80) REVERT: A 1035 ASN cc_start: 0.8167 (t0) cc_final: 0.7792 (t0) REVERT: A 1102 MET cc_start: 0.9052 (mtt) cc_final: 0.8532 (mtm) REVERT: A 1136 ARG cc_start: 0.8489 (mtp180) cc_final: 0.7710 (ttm110) REVERT: B 29 PHE cc_start: 0.8774 (t80) cc_final: 0.8297 (t80) REVERT: B 104 TYR cc_start: 0.9172 (p90) cc_final: 0.8662 (p90) outliers start: 28 outliers final: 19 residues processed: 208 average time/residue: 0.1915 time to fit residues: 56.3956 Evaluate side-chains 205 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1117 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.0070 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 50.0000 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9027 Z= 0.153 Angle : 0.555 7.853 12368 Z= 0.268 Chirality : 0.040 0.220 1481 Planarity : 0.004 0.034 1521 Dihedral : 10.249 122.234 1482 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.11 % Allowed : 20.05 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.07 (0.26), residues: 1114 helix: 1.10 (0.23), residues: 563 sheet: -0.43 (0.55), residues: 93 loop : -1.17 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.007 0.001 HIS A 936 PHE 0.022 0.001 PHE A1032 TYR 0.008 0.001 TYR A 179 ARG 0.004 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 206 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 ASP cc_start: 0.8875 (t0) cc_final: 0.8664 (t0) REVERT: A 265 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 284 ASN cc_start: 0.8995 (m110) cc_final: 0.8747 (m110) REVERT: A 301 LYS cc_start: 0.9242 (pttt) cc_final: 0.9007 (ptpp) REVERT: A 351 GLN cc_start: 0.8216 (mt0) cc_final: 0.7889 (mt0) REVERT: A 435 MET cc_start: 0.8162 (tpp) cc_final: 0.7710 (tpp) REVERT: A 499 ASP cc_start: 0.8179 (t70) cc_final: 0.7637 (t70) REVERT: A 892 ARG cc_start: 0.8242 (mmm-85) cc_final: 0.7786 (mmm160) REVERT: A 975 GLU cc_start: 0.8433 (tp30) cc_final: 0.7990 (tp30) REVERT: A 999 TYR cc_start: 0.8322 (m-10) cc_final: 0.7426 (m-80) REVERT: A 1035 ASN cc_start: 0.8185 (t0) cc_final: 0.7807 (t0) REVERT: A 1052 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8229 (mt-10) REVERT: A 1073 ILE cc_start: 0.8467 (mm) cc_final: 0.8190 (mt) REVERT: A 1081 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7589 (tt0) REVERT: A 1102 MET cc_start: 0.9017 (mtt) cc_final: 0.8682 (mtm) REVERT: A 1136 ARG cc_start: 0.8478 (mtp180) cc_final: 0.7372 (ttm110) REVERT: B 104 TYR cc_start: 0.9125 (p90) cc_final: 0.8641 (p90) outliers start: 27 outliers final: 21 residues processed: 216 average time/residue: 0.1816 time to fit residues: 56.4553 Evaluate side-chains 208 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain B residue 21 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9027 Z= 0.263 Angle : 0.604 7.763 12368 Z= 0.293 Chirality : 0.042 0.207 1481 Planarity : 0.004 0.033 1521 Dihedral : 10.260 121.132 1482 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.15 % Allowed : 21.31 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.13 (0.26), residues: 1114 helix: 1.17 (0.23), residues: 561 sheet: -0.44 (0.54), residues: 96 loop : -1.16 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1037 HIS 0.011 0.001 HIS A 936 PHE 0.023 0.002 PHE A1032 TYR 0.009 0.001 TYR A 995 ARG 0.005 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 196 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8313 (mp) cc_final: 0.8040 (mp) REVERT: A 265 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8021 (mt-10) REVERT: A 284 ASN cc_start: 0.9000 (m110) cc_final: 0.8724 (m110) REVERT: A 301 LYS cc_start: 0.9243 (pttt) cc_final: 0.9006 (ptpp) REVERT: A 351 GLN cc_start: 0.8269 (mt0) cc_final: 0.7937 (mt0) REVERT: A 443 MET cc_start: 0.8004 (mmm) cc_final: 0.6837 (mtp) REVERT: A 573 MET cc_start: 0.8531 (tmm) cc_final: 0.8133 (ttp) REVERT: A 892 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.7874 (mmm160) REVERT: A 975 GLU cc_start: 0.8465 (tp30) cc_final: 0.8011 (tp30) REVERT: A 999 TYR cc_start: 0.8420 (m-10) cc_final: 0.7586 (m-80) REVERT: A 1035 ASN cc_start: 0.8276 (t0) cc_final: 0.7831 (t0) REVERT: A 1073 ILE cc_start: 0.8536 (mm) cc_final: 0.8232 (mt) REVERT: A 1102 MET cc_start: 0.9039 (mtt) cc_final: 0.8557 (mtm) REVERT: A 1136 ARG cc_start: 0.8498 (mtp180) cc_final: 0.7686 (ttm110) REVERT: A 1139 PHE cc_start: 0.8921 (t80) cc_final: 0.8304 (t80) REVERT: B 104 TYR cc_start: 0.9151 (p90) cc_final: 0.8638 (p90) outliers start: 36 outliers final: 28 residues processed: 210 average time/residue: 0.1853 time to fit residues: 56.1672 Evaluate side-chains 218 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 57 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.0470 chunk 107 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 56 optimal weight: 0.0270 chunk 103 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN ** A 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9027 Z= 0.136 Angle : 0.564 7.290 12368 Z= 0.270 Chirality : 0.040 0.188 1481 Planarity : 0.004 0.033 1521 Dihedral : 9.989 122.644 1482 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.11 % Allowed : 23.04 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.27 (0.26), residues: 1114 helix: 1.33 (0.23), residues: 560 sheet: -0.26 (0.55), residues: 96 loop : -1.17 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.008 0.001 HIS A 936 PHE 0.025 0.001 PHE A1032 TYR 0.007 0.001 TYR A 995 ARG 0.007 0.000 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 210 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8354 (mp) cc_final: 0.8068 (mp) REVERT: A 121 ARG cc_start: 0.8558 (mtm-85) cc_final: 0.8205 (ptt180) REVERT: A 265 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8055 (mt-10) REVERT: A 284 ASN cc_start: 0.8999 (m110) cc_final: 0.8773 (m110) REVERT: A 301 LYS cc_start: 0.9241 (pttt) cc_final: 0.9003 (ptpp) REVERT: A 351 GLN cc_start: 0.8202 (mt0) cc_final: 0.7858 (mt0) REVERT: A 435 MET cc_start: 0.8164 (tpp) cc_final: 0.7722 (tpp) REVERT: A 443 MET cc_start: 0.7995 (mmm) cc_final: 0.6769 (mtp) REVERT: A 499 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7438 (t0) REVERT: A 769 ARG cc_start: 0.8588 (mtp180) cc_final: 0.8019 (mtt-85) REVERT: A 892 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.7822 (mmm160) REVERT: A 975 GLU cc_start: 0.8373 (tp30) cc_final: 0.7897 (tp30) REVERT: A 999 TYR cc_start: 0.8318 (m-10) cc_final: 0.7410 (m-80) REVERT: A 1035 ASN cc_start: 0.8224 (t0) cc_final: 0.7848 (t0) REVERT: A 1102 MET cc_start: 0.8986 (mtt) cc_final: 0.8620 (mtm) REVERT: A 1136 ARG cc_start: 0.8397 (mtp180) cc_final: 0.7299 (ttm110) REVERT: B 34 MET cc_start: 0.7656 (mtp) cc_final: 0.7270 (ptp) REVERT: B 104 TYR cc_start: 0.9092 (p90) cc_final: 0.8646 (p90) outliers start: 27 outliers final: 20 residues processed: 216 average time/residue: 0.1954 time to fit residues: 60.1463 Evaluate side-chains 212 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 57 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.0470 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9027 Z= 0.188 Angle : 0.600 10.759 12368 Z= 0.283 Chirality : 0.041 0.176 1481 Planarity : 0.004 0.033 1521 Dihedral : 9.906 120.923 1482 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.69 % Allowed : 23.96 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.35 (0.26), residues: 1114 helix: 1.36 (0.22), residues: 563 sheet: -0.23 (0.55), residues: 96 loop : -1.10 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1037 HIS 0.008 0.001 HIS A 936 PHE 0.024 0.001 PHE A1032 TYR 0.020 0.001 TYR A 179 ARG 0.006 0.000 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8483 (mp) cc_final: 0.8254 (mp) REVERT: A 220 CYS cc_start: 0.5722 (p) cc_final: 0.5225 (p) REVERT: A 265 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8047 (mt-10) REVERT: A 284 ASN cc_start: 0.9007 (m110) cc_final: 0.8773 (m110) REVERT: A 301 LYS cc_start: 0.9241 (pttt) cc_final: 0.9002 (ptpp) REVERT: A 351 GLN cc_start: 0.8213 (mt0) cc_final: 0.7829 (mt0) REVERT: A 443 MET cc_start: 0.7945 (mmm) cc_final: 0.6667 (mtp) REVERT: A 569 PHE cc_start: 0.8494 (m-10) cc_final: 0.8243 (m-10) REVERT: A 573 MET cc_start: 0.8248 (ttp) cc_final: 0.7824 (tmm) REVERT: A 769 ARG cc_start: 0.8618 (mtp180) cc_final: 0.8064 (mtt-85) REVERT: A 892 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7448 (mpp80) REVERT: A 975 GLU cc_start: 0.8417 (tp30) cc_final: 0.7932 (tp30) REVERT: A 999 TYR cc_start: 0.8374 (m-10) cc_final: 0.7479 (m-80) REVERT: A 1035 ASN cc_start: 0.8261 (t0) cc_final: 0.7867 (t0) REVERT: A 1102 MET cc_start: 0.8960 (mtt) cc_final: 0.8593 (mtm) REVERT: A 1136 ARG cc_start: 0.8414 (mtp180) cc_final: 0.7600 (ttm110) REVERT: B 104 TYR cc_start: 0.9057 (p90) cc_final: 0.8657 (p90) outliers start: 32 outliers final: 27 residues processed: 200 average time/residue: 0.1860 time to fit residues: 53.2210 Evaluate side-chains 208 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain B residue 57 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.0770 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.2980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9027 Z= 0.144 Angle : 0.580 10.499 12368 Z= 0.273 Chirality : 0.041 0.169 1481 Planarity : 0.004 0.033 1521 Dihedral : 9.708 122.315 1482 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.23 % Allowed : 24.08 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.42 (0.26), residues: 1114 helix: 1.43 (0.22), residues: 563 sheet: -0.17 (0.57), residues: 96 loop : -1.09 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.010 0.001 HIS A 936 PHE 0.025 0.001 PHE A1032 TYR 0.015 0.001 TYR A 179 ARG 0.006 0.000 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8389 (mp) cc_final: 0.8133 (mp) REVERT: A 121 ARG cc_start: 0.8539 (mtm-85) cc_final: 0.8289 (ptt180) REVERT: A 220 CYS cc_start: 0.5689 (p) cc_final: 0.5200 (p) REVERT: A 265 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8051 (mt-10) REVERT: A 284 ASN cc_start: 0.9008 (m110) cc_final: 0.8797 (m110) REVERT: A 301 LYS cc_start: 0.9243 (pttt) cc_final: 0.8997 (ptpp) REVERT: A 325 GLU cc_start: 0.8283 (pm20) cc_final: 0.7948 (pm20) REVERT: A 443 MET cc_start: 0.7930 (mmm) cc_final: 0.6646 (mtp) REVERT: A 529 ARG cc_start: 0.8386 (mtt-85) cc_final: 0.8157 (mtt-85) REVERT: A 569 PHE cc_start: 0.8476 (m-10) cc_final: 0.8200 (m-10) REVERT: A 769 ARG cc_start: 0.8599 (mtp180) cc_final: 0.8034 (mtt-85) REVERT: A 975 GLU cc_start: 0.8390 (tp30) cc_final: 0.7895 (tp30) REVERT: A 999 TYR cc_start: 0.8315 (m-10) cc_final: 0.7416 (m-80) REVERT: A 1035 ASN cc_start: 0.8248 (t0) cc_final: 0.7868 (t0) REVERT: A 1102 MET cc_start: 0.8928 (mtt) cc_final: 0.8654 (mtm) REVERT: A 1136 ARG cc_start: 0.8393 (mtp180) cc_final: 0.7293 (ttm110) REVERT: B 63 VAL cc_start: 0.7667 (t) cc_final: 0.7323 (p) REVERT: B 104 TYR cc_start: 0.9008 (p90) cc_final: 0.8598 (p90) REVERT: B 105 ARG cc_start: 0.8552 (mmt90) cc_final: 0.8086 (mmt90) outliers start: 28 outliers final: 18 residues processed: 208 average time/residue: 0.1921 time to fit residues: 56.9531 Evaluate side-chains 206 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 188 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain B residue 57 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9027 Z= 0.238 Angle : 0.626 9.650 12368 Z= 0.299 Chirality : 0.041 0.158 1481 Planarity : 0.004 0.031 1521 Dihedral : 9.629 120.648 1482 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.76 % Allowed : 25.58 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.46 (0.26), residues: 1114 helix: 1.48 (0.22), residues: 563 sheet: -0.29 (0.57), residues: 93 loop : -1.06 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 108 HIS 0.007 0.001 HIS A 809 PHE 0.026 0.002 PHE A1032 TYR 0.013 0.001 TYR A 179 ARG 0.006 0.000 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 190 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6491 (mt) REVERT: A 92 LEU cc_start: 0.8315 (mp) cc_final: 0.8073 (mp) REVERT: A 220 CYS cc_start: 0.5739 (p) cc_final: 0.5267 (p) REVERT: A 223 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7803 (mm-30) REVERT: A 265 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8045 (mt-10) REVERT: A 284 ASN cc_start: 0.9006 (m110) cc_final: 0.8778 (m110) REVERT: A 301 LYS cc_start: 0.9252 (pttt) cc_final: 0.9007 (ptpp) REVERT: A 443 MET cc_start: 0.7984 (mmm) cc_final: 0.6712 (mtp) REVERT: A 529 ARG cc_start: 0.8409 (mtt-85) cc_final: 0.8167 (mtt-85) REVERT: A 892 ARG cc_start: 0.8163 (mmm-85) cc_final: 0.7473 (mpp80) REVERT: A 975 GLU cc_start: 0.8439 (tp30) cc_final: 0.7934 (tp30) REVERT: A 999 TYR cc_start: 0.8399 (m-10) cc_final: 0.7539 (m-80) REVERT: A 1035 ASN cc_start: 0.8325 (t0) cc_final: 0.7895 (t0) REVERT: A 1102 MET cc_start: 0.8952 (mtt) cc_final: 0.8507 (mtm) REVERT: A 1136 ARG cc_start: 0.8443 (mtp180) cc_final: 0.7384 (ttm110) REVERT: B 63 VAL cc_start: 0.7470 (t) cc_final: 0.7102 (p) REVERT: B 104 TYR cc_start: 0.9043 (p90) cc_final: 0.8627 (p90) REVERT: B 105 ARG cc_start: 0.8542 (mmt90) cc_final: 0.8303 (mmt90) REVERT: B 108 TRP cc_start: 0.8190 (m100) cc_final: 0.7938 (m100) outliers start: 24 outliers final: 20 residues processed: 199 average time/residue: 0.1791 time to fit residues: 51.3956 Evaluate side-chains 207 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain B residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 40.0000 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9027 Z= 0.156 Angle : 0.595 10.069 12368 Z= 0.282 Chirality : 0.040 0.161 1481 Planarity : 0.004 0.034 1521 Dihedral : 9.263 122.121 1482 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.30 % Allowed : 26.96 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.52 (0.26), residues: 1114 helix: 1.52 (0.22), residues: 565 sheet: -0.21 (0.58), residues: 93 loop : -1.04 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.006 0.001 HIS A 809 PHE 0.026 0.001 PHE A1032 TYR 0.011 0.001 TYR A 179 ARG 0.006 0.000 ARG A 427 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6385 (mt) REVERT: A 92 LEU cc_start: 0.8258 (mp) cc_final: 0.8053 (mp) REVERT: A 121 ARG cc_start: 0.8487 (mtm-85) cc_final: 0.8277 (ptt180) REVERT: A 220 CYS cc_start: 0.5678 (p) cc_final: 0.5219 (p) REVERT: A 284 ASN cc_start: 0.9020 (m110) cc_final: 0.8804 (m110) REVERT: A 301 LYS cc_start: 0.9227 (pttt) cc_final: 0.8982 (ptpp) REVERT: A 416 ILE cc_start: 0.8625 (mm) cc_final: 0.8276 (pt) REVERT: A 443 MET cc_start: 0.7974 (mmm) cc_final: 0.6699 (mtp) REVERT: A 529 ARG cc_start: 0.8375 (mtt-85) cc_final: 0.8150 (mtt-85) REVERT: A 569 PHE cc_start: 0.8532 (m-10) cc_final: 0.8278 (m-10) REVERT: A 975 GLU cc_start: 0.8426 (tp30) cc_final: 0.7915 (tp30) REVERT: A 999 TYR cc_start: 0.8339 (m-10) cc_final: 0.7440 (m-80) REVERT: A 1035 ASN cc_start: 0.8253 (t0) cc_final: 0.7876 (t0) REVERT: A 1102 MET cc_start: 0.8899 (mtt) cc_final: 0.8643 (mtm) REVERT: A 1136 ARG cc_start: 0.8409 (mtp180) cc_final: 0.7373 (ttm110) REVERT: B 63 VAL cc_start: 0.7243 (t) cc_final: 0.6841 (p) REVERT: B 104 TYR cc_start: 0.9053 (p90) cc_final: 0.8688 (p90) REVERT: B 105 ARG cc_start: 0.8552 (mmt90) cc_final: 0.8072 (mmt90) REVERT: B 108 TRP cc_start: 0.8302 (m100) cc_final: 0.8021 (m100) outliers start: 20 outliers final: 15 residues processed: 196 average time/residue: 0.1851 time to fit residues: 52.4095 Evaluate side-chains 200 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.0870 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 HIS ** 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 = 0.3798 r_free = 0.3798 target = 0.141614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111450 restraints weight = 15290.075| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 4.00 r_work: 0.3230 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9027 Z= 0.213 Angle : 0.609 9.354 12368 Z= 0.290 Chirality : 0.041 0.154 1481 Planarity : 0.004 0.031 1521 Dihedral : 9.082 120.596 1482 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.30 % Allowed : 26.73 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.56 (0.26), residues: 1114 helix: 1.57 (0.23), residues: 563 sheet: -0.26 (0.56), residues: 96 loop : -1.00 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.005 0.001 HIS A 936 PHE 0.026 0.002 PHE A1032 TYR 0.012 0.001 TYR A 179 ARG 0.004 0.000 ARG B 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2167.43 seconds wall clock time: 39 minutes 56.20 seconds (2396.20 seconds total)