Starting phenix.real_space_refine on Fri Jul 19 14:42:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8js8_36616/07_2024/8js8_36616.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8js8_36616/07_2024/8js8_36616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8js8_36616/07_2024/8js8_36616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8js8_36616/07_2024/8js8_36616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8js8_36616/07_2024/8js8_36616.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8js8_36616/07_2024/8js8_36616.cif" } resolution = 2.88 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= 0.001 sd= 1.121 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 5291 2.51 5 N 1362 2.21 5 O 1489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 147": "OE1" <-> "OE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 538": "OD1" <-> "OD2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A ASP 680": "OD1" <-> "OD2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1009": "OD1" <-> "OD2" Residue "B ASP 1058": "OD1" <-> "OD2" Residue "B ASP 1089": "OD1" <-> "OD2" Residue "B ASP 1099": "OD1" <-> "OD2" Residue "B ASP 1108": "OD1" <-> "OD2" Residue "B TYR 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1171": "OD1" <-> "OD2" Residue "B GLU 1210": "OE1" <-> "OE2" Residue "B PHE 1249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1288": "OD1" <-> "OD2" Residue "B ASP 1289": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8189 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4674 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 576} Chain breaks: 1 Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3437 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'UKX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.49, per 1000 atoms: 0.67 Number of scatterers: 8189 At special positions: 0 Unit cell: (88.81, 84.66, 147.74, 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 1489 8.00 N 1362 7.00 C 5291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 F 1 " - " NAG F 2 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 498 " " NAG A 802 " - " ASN A 548 " " NAG F 1 " - " ASN A 573 " Time building additional restraints: 3.92 Conformation dependent library (CDL) restraints added in 2.8 seconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 137 through 160 Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.734A pdb=" N ASP A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 198 Proline residue: A 191 - end of helix removed outlier: 4.327A pdb=" N LYS A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 4.554A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N TYR A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 220 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 250 Processing helix chain 'A' and resid 255 through 271 removed outlier: 4.339A pdb=" N GLY A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.712A pdb=" N ILE A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 284 No H-bonds generated for 'chain 'A' and resid 283 through 284' Processing helix chain 'A' and resid 285 through 288 removed outlier: 3.782A pdb=" N LYS A 288 " --> pdb=" O ALA A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.969A pdb=" N MET A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.741A pdb=" N VAL A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.578A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 386 Processing helix chain 'A' and resid 419 through 439 removed outlier: 3.521A pdb=" N PHE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 483 Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 593 through 619 removed outlier: 3.777A pdb=" N VAL A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) Proline residue: A 610 - end of helix removed outlier: 3.516A pdb=" N ILE A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 641 removed outlier: 3.628A pdb=" N MET A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.812A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 706 Processing helix chain 'A' and resid 712 through 731 removed outlier: 3.925A pdb=" N ILE A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.854A pdb=" N VAL B 933 " --> pdb=" O ASN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 958 Processing helix chain 'B' and resid 1080 through 1092 Processing helix chain 'B' and resid 1265 through 1273 Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 492 removed outlier: 6.247A pdb=" N GLY A 509 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG A 491 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A 511 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR A 500 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU A 521 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU A 502 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER A 523 " --> pdb=" O GLU A 502 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 515 through 527 current: chain 'A' and resid 550 through 552 removed outlier: 6.242A pdb=" N PHE A 551 " --> pdb=" O ILE A 572 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 567 removed outlier: 6.031A pdb=" N PHE A 546 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 545 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR A 500 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU A 521 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU A 502 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER A 523 " --> pdb=" O GLU A 502 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 500 through 512 current: chain 'A' and resid 555 through 559 Processing sheet with id=AA3, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.556A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B1074 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER B 880 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE B1072 " --> pdb=" O SER B 880 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N VAL B 882 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N LYS B1070 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 16.599A pdb=" N LYS B 884 " --> pdb=" O MET B1068 " (cutoff:3.500A) removed outlier: 18.261A pdb=" N MET B1068 " --> pdb=" O LYS B 884 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.556A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B1074 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER B 880 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE B1072 " --> pdb=" O SER B 880 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N VAL B 882 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N LYS B1070 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 16.599A pdb=" N LYS B 884 " --> pdb=" O MET B1068 " (cutoff:3.500A) removed outlier: 18.261A pdb=" N MET B1068 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE B1069 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LYS B 948 " --> pdb=" O ILE B1069 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR B1071 " --> pdb=" O TRP B 946 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP B 946 " --> pdb=" O TYR B1071 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 897 through 900 Processing sheet with id=AA6, first strand: chain 'B' and resid 962 through 968 removed outlier: 6.839A pdb=" N VAL B 976 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASN B 966 " --> pdb=" O TRP B 974 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TRP B 974 " --> pdb=" O ASN B 966 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id=AA8, first strand: chain 'B' and resid 1122 through 1125 Processing sheet with id=AA9, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 3.977A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS B1226 " --> pdb=" O LYS B1234 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LYS B1234 " --> pdb=" O LYS B1226 " (cutoff:3.500A) removed outlier: 27.362A pdb=" N ASN B1233 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 23.576A pdb=" N LEU B1254 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 16.011A pdb=" N CYS B1235 " --> pdb=" O PHE B1252 " (cutoff:3.500A) removed outlier: 11.284A pdb=" N PHE B1252 " --> pdb=" O CYS B1235 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B1204 " --> pdb=" O ALA B1263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 3.977A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1227 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: 2.89 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2017 1.33 - 1.45: 1766 1.45 - 1.57: 4524 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8383 Sorted by residual: bond pdb=" C5 UKX A 803 " pdb=" N2 UKX A 803 " ideal model delta sigma weight residual 1.340 1.390 -0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" C1 UKX A 803 " pdb=" N1 UKX A 803 " ideal model delta sigma weight residual 1.353 1.396 -0.043 2.00e-02 2.50e+03 4.58e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C ILE A 315 " pdb=" N PRO A 316 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.19e-02 7.06e+03 3.39e+00 bond pdb=" C6 UKX A 803 " pdb=" C7 UKX A 803 " ideal model delta sigma weight residual 1.523 1.548 -0.025 2.00e-02 2.50e+03 1.57e+00 ... (remaining 8378 not shown) Histogram of bond angle deviations from ideal: 97.96 - 105.18: 98 105.18 - 112.40: 4115 112.40 - 119.61: 2793 119.61 - 126.83: 4221 126.83 - 134.05: 108 Bond angle restraints: 11335 Sorted by residual: angle pdb=" N GLY B1157 " pdb=" CA GLY B1157 " pdb=" C GLY B1157 " ideal model delta sigma weight residual 111.56 115.41 -3.85 1.01e+00 9.80e-01 1.45e+01 angle pdb=" CA ARG A 141 " pdb=" CB ARG A 141 " pdb=" CG ARG A 141 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 angle pdb=" C GLU B1210 " pdb=" N ILE B1211 " pdb=" CA ILE B1211 " ideal model delta sigma weight residual 120.33 123.10 -2.77 8.00e-01 1.56e+00 1.20e+01 angle pdb=" CB ARG A 141 " pdb=" CG ARG A 141 " pdb=" CD ARG A 141 " ideal model delta sigma weight residual 111.30 118.74 -7.44 2.30e+00 1.89e-01 1.05e+01 angle pdb=" CA ARG A 491 " pdb=" CB ARG A 491 " pdb=" CG ARG A 491 " ideal model delta sigma weight residual 114.10 120.20 -6.10 2.00e+00 2.50e-01 9.30e+00 ... (remaining 11330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 4278 16.39 - 32.78: 468 32.78 - 49.17: 173 49.17 - 65.55: 31 65.55 - 81.94: 14 Dihedral angle restraints: 4964 sinusoidal: 2041 harmonic: 2923 Sorted by residual: dihedral pdb=" CA MET B 937 " pdb=" C MET B 937 " pdb=" N TYR B 938 " pdb=" CA TYR B 938 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLN B1219 " pdb=" C GLN B1219 " pdb=" N VAL B1220 " pdb=" CA VAL B1220 " ideal model delta harmonic sigma weight residual 180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA PHE A 497 " pdb=" C PHE A 497 " pdb=" N ASN A 498 " pdb=" CA ASN A 498 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 4961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1035 0.057 - 0.113: 186 0.113 - 0.170: 18 0.170 - 0.226: 2 0.226 - 0.283: 3 Chirality restraints: 1244 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 498 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 548 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C6 UKX A 803 " pdb=" C5 UKX A 803 " pdb=" C7 UKX A 803 " pdb=" N1 UKX A 803 " both_signs ideal model delta sigma weight residual False 2.45 2.69 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1241 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B1117 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C PHE B1117 " 0.025 2.00e-02 2.50e+03 pdb=" O PHE B1117 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP B1118 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 938 " 0.008 2.00e-02 2.50e+03 9.69e-03 1.88e+00 pdb=" CG TYR B 938 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 938 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 938 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 938 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 938 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 938 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 938 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 602 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C PHE A 602 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE A 602 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU A 603 " 0.008 2.00e-02 2.50e+03 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 410 2.73 - 3.27: 8086 3.27 - 3.82: 13720 3.82 - 4.36: 16679 4.36 - 4.90: 29111 Nonbonded interactions: 68006 Sorted by model distance: nonbonded pdb=" OH TYR A 279 " pdb=" O PRO A 355 " model vdw 2.188 2.440 nonbonded pdb=" NE2 GLN A 323 " pdb=" O GLY A 325 " model vdw 2.232 2.520 nonbonded pdb=" ND2 ASN B 918 " pdb=" O ASP B1062 " model vdw 2.248 2.520 nonbonded pdb=" NH2 ARG A 145 " pdb=" O GLN A 742 " model vdw 2.250 2.520 nonbonded pdb=" O TRP B1266 " pdb=" NE2 GLN B1270 " model vdw 2.268 2.520 ... (remaining 68001 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: 1.510 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 28.370 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.003 0.050 8383 Z= 0.205 Angle : 0.613 9.718 11335 Z= 0.338 Chirality : 0.045 0.283 1244 Planarity : 0.003 0.041 1428 Dihedral : 16.363 81.943 3098 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.28 % Allowed : 19.45 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 1006 helix: 1.75 (0.25), residues: 408 sheet: 0.32 (0.35), residues: 239 loop : -1.08 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 300 HIS 0.005 0.001 HIS A 494 PHE 0.017 0.001 PHE A 512 TYR 0.023 0.001 TYR B 938 ARG 0.011 0.001 ARG B1064 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.917 Fit side-chains REVERT: A 379 ASP cc_start: 0.7003 (m-30) cc_final: 0.6546 (p0) REVERT: B 937 MET cc_start: 0.4649 (OUTLIER) cc_final: 0.4298 (pp-130) REVERT: B 1058 ASP cc_start: 0.6456 (OUTLIER) cc_final: 0.5889 (m-30) outliers start: 20 outliers final: 15 residues processed: 142 average time/residue: 1.0892 time to fit residues: 165.1994 Evaluate side-chains 144 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1218 SER Chi-restraints excluded: chain B residue 1247 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 387 HIS A 434 ASN A 568 ASN B 970 ASN B1003 GLN B1038 GLN B1091 GLN B1093 ASN B1199 GLN B1257 ASN B1265 ASN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8383 Z= 0.197 Angle : 0.514 6.029 11335 Z= 0.276 Chirality : 0.043 0.260 1244 Planarity : 0.003 0.028 1428 Dihedral : 6.853 53.874 1249 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.19 % Allowed : 17.41 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.27), residues: 1006 helix: 2.21 (0.25), residues: 411 sheet: 0.26 (0.34), residues: 244 loop : -1.01 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 467 HIS 0.005 0.001 HIS A 494 PHE 0.014 0.001 PHE A 512 TYR 0.016 0.001 TYR B 938 ARG 0.006 0.000 ARG B1064 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: B 937 MET cc_start: 0.4835 (OUTLIER) cc_final: 0.4601 (pp-130) REVERT: B 1003 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: B 1028 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8030 (mttp) outliers start: 28 outliers final: 12 residues processed: 149 average time/residue: 1.0866 time to fit residues: 172.9646 Evaluate side-chains 147 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1209 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 62 optimal weight: 0.0020 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 0.2980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 970 ASN B1003 GLN B1038 GLN B1199 GLN B1257 ASN B1265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8383 Z= 0.164 Angle : 0.477 6.021 11335 Z= 0.257 Chirality : 0.043 0.295 1244 Planarity : 0.003 0.032 1428 Dihedral : 5.646 47.022 1231 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.30 % Allowed : 17.86 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.07 (0.27), residues: 1006 helix: 2.35 (0.25), residues: 413 sheet: 0.23 (0.35), residues: 240 loop : -0.93 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 PHE 0.009 0.001 PHE A 459 TYR 0.012 0.001 TYR A 306 ARG 0.008 0.000 ARG B1064 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 0.890 Fit side-chains REVERT: A 515 LYS cc_start: 0.7815 (ptpp) cc_final: 0.7536 (ptpp) REVERT: B 1003 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: B 1052 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7074 (ttpp) REVERT: B 1083 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7352 (mt-10) REVERT: B 1165 TYR cc_start: 0.6891 (t80) cc_final: 0.6663 (t80) outliers start: 29 outliers final: 12 residues processed: 158 average time/residue: 1.1930 time to fit residues: 200.6879 Evaluate side-chains 151 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1052 LYS Chi-restraints excluded: chain B residue 1209 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.0050 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 960 ASN B 970 ASN B1003 GLN B1038 GLN B1233 ASN B1257 ASN B1265 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8383 Z= 0.163 Angle : 0.472 5.827 11335 Z= 0.254 Chirality : 0.042 0.277 1244 Planarity : 0.003 0.031 1428 Dihedral : 5.181 47.442 1224 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.64 % Allowed : 17.86 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1006 helix: 2.39 (0.25), residues: 413 sheet: 0.26 (0.35), residues: 230 loop : -0.90 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 467 HIS 0.004 0.001 HIS A 387 PHE 0.016 0.001 PHE A 512 TYR 0.012 0.001 TYR A 306 ARG 0.009 0.000 ARG B1064 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 0.920 Fit side-chains REVERT: A 522 LYS cc_start: 0.7928 (tppt) cc_final: 0.7543 (ttpp) REVERT: B 1003 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: B 1052 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7076 (ttpp) REVERT: B 1083 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7363 (mt-10) REVERT: B 1165 TYR cc_start: 0.6963 (t80) cc_final: 0.6722 (t80) outliers start: 32 outliers final: 18 residues processed: 153 average time/residue: 1.1151 time to fit residues: 182.4005 Evaluate side-chains 150 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1052 LYS Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1209 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN B 970 ASN B1003 GLN B1199 GLN B1257 ASN B1265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8383 Z= 0.188 Angle : 0.484 6.455 11335 Z= 0.259 Chirality : 0.043 0.273 1244 Planarity : 0.003 0.035 1428 Dihedral : 5.112 47.049 1224 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.96 % Allowed : 19.91 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.10 (0.27), residues: 1006 helix: 2.37 (0.25), residues: 413 sheet: 0.25 (0.35), residues: 230 loop : -0.89 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 PHE 0.009 0.001 PHE A 459 TYR 0.014 0.001 TYR A 306 ARG 0.011 0.000 ARG B1064 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 0.995 Fit side-chains REVERT: A 634 MET cc_start: 0.7719 (mmt) cc_final: 0.7507 (mmm) REVERT: B 882 VAL cc_start: 0.7726 (m) cc_final: 0.7458 (p) REVERT: B 1052 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7091 (ttpp) REVERT: B 1058 ASP cc_start: 0.6580 (OUTLIER) cc_final: 0.5995 (m-30) REVERT: B 1083 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7375 (mt-10) REVERT: B 1165 TYR cc_start: 0.6926 (t80) cc_final: 0.6695 (t80) outliers start: 26 outliers final: 18 residues processed: 143 average time/residue: 1.1384 time to fit residues: 173.6377 Evaluate side-chains 150 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1052 LYS Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1209 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 364 ASN A 387 HIS A 513 ASN A 646 ASN B 970 ASN B1003 GLN B1219 GLN B1257 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8383 Z= 0.317 Angle : 0.559 5.607 11335 Z= 0.297 Chirality : 0.046 0.301 1244 Planarity : 0.003 0.029 1428 Dihedral : 5.360 49.620 1224 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.10 % Allowed : 19.57 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.84 (0.27), residues: 1006 helix: 2.13 (0.25), residues: 407 sheet: 0.28 (0.35), residues: 236 loop : -1.09 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 467 HIS 0.005 0.001 HIS A 387 PHE 0.016 0.002 PHE A 512 TYR 0.020 0.002 TYR A 306 ARG 0.009 0.001 ARG B1064 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 0.916 Fit side-chains REVERT: A 252 VAL cc_start: 0.6557 (OUTLIER) cc_final: 0.6309 (p) REVERT: A 634 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7573 (mmm) REVERT: B 925 GLU cc_start: 0.6220 (mm-30) cc_final: 0.5783 (tp30) REVERT: B 1083 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7336 (mt-10) outliers start: 36 outliers final: 20 residues processed: 164 average time/residue: 1.0993 time to fit residues: 192.4487 Evaluate side-chains 159 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1204 LYS Chi-restraints excluded: chain B residue 1209 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 513 ASN B 970 ASN B1003 GLN B1219 GLN B1257 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8383 Z= 0.259 Angle : 0.535 7.268 11335 Z= 0.285 Chirality : 0.045 0.289 1244 Planarity : 0.003 0.037 1428 Dihedral : 5.265 52.259 1223 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.32 % Allowed : 20.25 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.85 (0.27), residues: 1006 helix: 2.11 (0.25), residues: 410 sheet: 0.28 (0.35), residues: 236 loop : -1.06 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 467 HIS 0.005 0.001 HIS A 387 PHE 0.010 0.001 PHE A 499 TYR 0.016 0.002 TYR A 306 ARG 0.011 0.000 ARG B1064 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 139 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 252 VAL cc_start: 0.6486 (OUTLIER) cc_final: 0.6255 (p) REVERT: A 382 MET cc_start: 0.7124 (mmt) cc_final: 0.6841 (mpt) REVERT: B 903 ARG cc_start: 0.7549 (mtp180) cc_final: 0.7292 (mmm160) REVERT: B 1003 GLN cc_start: 0.9426 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: B 1083 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7348 (mt-10) outliers start: 38 outliers final: 25 residues processed: 163 average time/residue: 1.1363 time to fit residues: 197.2852 Evaluate side-chains 166 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1204 LYS Chi-restraints excluded: chain B residue 1209 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 61 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 513 ASN B 970 ASN B1003 GLN B1219 GLN B1257 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8383 Z= 0.190 Angle : 0.508 6.813 11335 Z= 0.271 Chirality : 0.043 0.276 1244 Planarity : 0.003 0.044 1428 Dihedral : 5.136 52.275 1223 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.10 % Allowed : 20.48 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.01 (0.27), residues: 1006 helix: 2.28 (0.25), residues: 411 sheet: 0.27 (0.36), residues: 230 loop : -0.95 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 467 HIS 0.005 0.001 HIS A 387 PHE 0.017 0.001 PHE A 512 TYR 0.017 0.001 TYR B1001 ARG 0.013 0.000 ARG B1064 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 139 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 903 ARG cc_start: 0.7514 (mtp180) cc_final: 0.7271 (mmm160) REVERT: B 1003 GLN cc_start: 0.9426 (OUTLIER) cc_final: 0.8602 (tt0) REVERT: B 1054 MET cc_start: 0.7496 (tpt) cc_final: 0.7016 (tpt) REVERT: B 1058 ASP cc_start: 0.6799 (OUTLIER) cc_final: 0.6203 (m-30) REVERT: B 1083 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7342 (mt-10) outliers start: 36 outliers final: 23 residues processed: 159 average time/residue: 1.1558 time to fit residues: 195.7429 Evaluate side-chains 161 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 907 ASP Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1204 LYS Chi-restraints excluded: chain B residue 1209 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.7980 chunk 93 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 95 optimal weight: 0.2980 chunk 58 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 513 ASN B 970 ASN B1003 GLN B1257 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8383 Z= 0.186 Angle : 0.502 7.634 11335 Z= 0.268 Chirality : 0.043 0.269 1244 Planarity : 0.003 0.042 1428 Dihedral : 5.076 51.580 1223 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.64 % Allowed : 20.82 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.09 (0.27), residues: 1006 helix: 2.35 (0.25), residues: 411 sheet: 0.28 (0.36), residues: 230 loop : -0.88 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 PHE 0.009 0.001 PHE A 459 TYR 0.015 0.001 TYR B1001 ARG 0.011 0.000 ARG B1064 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 VAL cc_start: 0.6443 (OUTLIER) cc_final: 0.6235 (p) REVERT: A 382 MET cc_start: 0.7053 (mmt) cc_final: 0.6802 (mpt) REVERT: B 903 ARG cc_start: 0.7537 (mtp180) cc_final: 0.7271 (mmm160) REVERT: B 1052 LYS cc_start: 0.7585 (ttpp) cc_final: 0.7054 (ttpp) REVERT: B 1054 MET cc_start: 0.7481 (tpt) cc_final: 0.6947 (tpt) REVERT: B 1058 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.6196 (m-30) REVERT: B 1083 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7340 (mt-10) outliers start: 32 outliers final: 22 residues processed: 153 average time/residue: 1.2030 time to fit residues: 196.8408 Evaluate side-chains 162 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 911 LYS Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1204 LYS Chi-restraints excluded: chain B residue 1209 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 overall best weight: 0.3018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 513 ASN B 970 ASN B1003 GLN B1257 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8383 Z= 0.145 Angle : 0.488 10.907 11335 Z= 0.257 Chirality : 0.042 0.245 1244 Planarity : 0.003 0.042 1428 Dihedral : 4.805 48.434 1223 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.93 % Allowed : 22.75 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.27 (0.27), residues: 1006 helix: 2.50 (0.25), residues: 412 sheet: 0.28 (0.36), residues: 229 loop : -0.73 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 PHE 0.017 0.001 PHE A 512 TYR 0.015 0.001 TYR B1181 ARG 0.010 0.000 ARG B1064 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 0.942 Fit side-chains REVERT: A 227 ASP cc_start: 0.8170 (m-30) cc_final: 0.7884 (m-30) REVERT: A 382 MET cc_start: 0.6952 (mmt) cc_final: 0.6673 (mpt) REVERT: B 882 VAL cc_start: 0.7743 (m) cc_final: 0.7470 (p) REVERT: B 903 ARG cc_start: 0.7510 (mtp180) cc_final: 0.7278 (mmm160) REVERT: B 992 GLN cc_start: 0.8490 (mt0) cc_final: 0.8040 (mm-40) REVERT: B 1003 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: B 1054 MET cc_start: 0.7390 (tpt) cc_final: 0.6842 (tpt) REVERT: B 1058 ASP cc_start: 0.6686 (OUTLIER) cc_final: 0.6054 (m-30) REVERT: B 1083 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7320 (mt-10) outliers start: 17 outliers final: 10 residues processed: 151 average time/residue: 1.0710 time to fit residues: 172.9578 Evaluate side-chains 141 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1209 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 82 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 513 ASN B 970 ASN B1257 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.176017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136129 restraints weight = 9057.230| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.24 r_work: 0.3250 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8383 Z= 0.180 Angle : 0.500 9.886 11335 Z= 0.264 Chirality : 0.043 0.248 1244 Planarity : 0.003 0.040 1428 Dihedral : 4.798 47.654 1223 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.93 % Allowed : 23.21 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.30 (0.27), residues: 1006 helix: 2.53 (0.25), residues: 411 sheet: 0.33 (0.36), residues: 226 loop : -0.73 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 467 HIS 0.006 0.001 HIS A 387 PHE 0.009 0.001 PHE A 459 TYR 0.020 0.001 TYR B1255 ARG 0.011 0.000 ARG B1064 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3660.70 seconds wall clock time: 64 minutes 29.65 seconds (3869.65 seconds total)