Starting phenix.real_space_refine on Fri Mar 15 08:53:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxb_17263/03_2024/8oxb_17263_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxb_17263/03_2024/8oxb_17263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxb_17263/03_2024/8oxb_17263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxb_17263/03_2024/8oxb_17263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxb_17263/03_2024/8oxb_17263_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxb_17263/03_2024/8oxb_17263_updated.pdb" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 1 5.49 5 Mg 1 5.21 5 S 54 5.16 5 C 7198 2.51 5 N 1833 2.21 5 O 2049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 159": "OD1" <-> "OD2" Residue "A TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A ASP 641": "OD1" <-> "OD2" Residue "A ASP 644": "OD1" <-> "OD2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1116": "OD1" <-> "OD2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 121": "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: 11137 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8361 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 25, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2642 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 25, 'TRANS': 302} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' MG': 1, 'POV': 1, 'VN4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 6.25, per 1000 atoms: 0.56 Number of scatterers: 11137 At special positions: 0 Unit cell: (84.11, 97.7779, 176.631, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 54 16.00 P 1 15.00 Mg 1 11.99 O 2049 8.00 N 1833 7.00 C 7198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.04 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=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG C 1 " - " ASN B 180 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.80 Conformation dependent library (CDL) restraints added in 2.2 seconds 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2572 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 11 sheets defined 44.8% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 108 through 115 removed outlier: 4.189A pdb=" N GLN A 115 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 142 through 174 Proline residue: A 147 - end of helix removed outlier: 3.841A pdb=" N THR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 244 through 247 No H-bonds generated for 'chain 'A' and resid 244 through 247' Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 318 through 321 No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 332 through 369 removed outlier: 3.605A pdb=" N TYR A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE A 344 " --> pdb=" O MET A 340 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 381 through 395 removed outlier: 3.965A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 400 Processing helix chain 'A' and resid 402 through 420 removed outlier: 4.250A pdb=" N GLU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.792A pdb=" N ASN A 442 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLU A 443 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 553 through 564 Processing helix chain 'A' and resid 622 through 628 removed outlier: 3.635A pdb=" N GLU A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 648 Processing helix chain 'A' and resid 663 through 677 removed outlier: 3.592A pdb=" N TRP A 669 " --> pdb=" O GLU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 694 removed outlier: 3.696A pdb=" N GLU A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 722 Processing helix chain 'A' and resid 736 through 745 Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.588A pdb=" N SER A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 Processing helix chain 'A' and resid 803 through 810 removed outlier: 3.505A pdb=" N GLU A 808 " --> pdb=" O SER A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 858 Processing helix chain 'A' and resid 870 through 884 removed outlier: 3.669A pdb=" N ALA A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 removed outlier: 3.560A pdb=" N VAL A 898 " --> pdb=" O ALA A 895 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN A 899 " --> pdb=" O ASN A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 937 removed outlier: 3.572A pdb=" N LEU A 935 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 936 " --> pdb=" O GLN A 933 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 937 " --> pdb=" O ARG A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 962 Processing helix chain 'A' and resid 964 through 971 removed outlier: 4.273A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE A 971 " --> pdb=" O TRP A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 Processing helix chain 'A' and resid 995 through 1000 Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1016 through 1023 Processing helix chain 'A' and resid 1030 through 1056 Proline residue: A1051 - end of helix Processing helix chain 'A' and resid 1069 through 1091 removed outlier: 3.637A pdb=" N GLY A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1113 removed outlier: 3.538A pdb=" N ILE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1141 removed outlier: 3.726A pdb=" N LEU A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A1141 " --> pdb=" O SER A1137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1136 through 1141' Processing helix chain 'A' and resid 1143 through 1170 Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1174 through 1180 Processing helix chain 'B' and resid 47 through 74 removed outlier: 3.607A pdb=" N LEU B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix removed outlier: 3.911A pdb=" N ILE B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 92 through 96 removed outlier: 3.813A pdb=" N SER B 96 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 135 No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 140 through 143 No H-bonds generated for 'chain 'B' and resid 140 through 143' Processing helix chain 'B' and resid 147 through 150 No H-bonds generated for 'chain 'B' and resid 147 through 150' Processing helix chain 'B' and resid 155 through 160 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 223 through 226 No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 323 through 349 Processing sheet with id= A, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.505A pdb=" N TRP A 64 " --> pdb=" O CYS A 265 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 179 through 181 Processing sheet with id= C, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.867A pdb=" N ASP A 211 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.976A pdb=" N TYR A 225 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 277 through 281 removed outlier: 4.412A pdb=" N GLY A 277 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 906 through 909 removed outlier: 6.414A pdb=" N TYR A 450 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A 891 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE A 452 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS A 727 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N SER A 453 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TRP A 729 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A 863 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR A 754 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE A 800 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N CYS A 756 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR A 802 " --> pdb=" O CYS A 756 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 584 through 588 removed outlier: 3.538A pdb=" N ALA A 571 " --> pdb=" O THR A 578 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER A 580 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N PHE A 569 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 699 through 703 removed outlier: 6.824A pdb=" N LEU A 656 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 592 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG A 608 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL A 590 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 464 through 469 removed outlier: 6.685A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 77 through 81 removed outlier: 3.525A pdb=" N ARG B 307 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N TYR B 122 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU B 272 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU B 124 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ARG B 270 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 102 through 110 removed outlier: 4.047A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 182 " --> pdb=" O THR B 296 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 5.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1783 1.31 - 1.43: 3158 1.43 - 1.56: 6353 1.56 - 1.69: 6 1.69 - 1.81: 83 Bond restraints: 11383 Sorted by residual: bond pdb=" C31 POV A1203 " pdb=" O31 POV A1203 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C21 POV A1203 " pdb=" O21 POV A1203 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" N POV A1203 " pdb=" C12 POV A1203 " ideal model delta sigma weight residual 1.508 1.465 0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.561 -0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" N POV A1203 " pdb=" C15 POV A1203 " ideal model delta sigma weight residual 1.491 1.455 0.036 2.00e-02 2.50e+03 3.17e+00 ... (remaining 11378 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.55: 257 106.55 - 113.42: 6175 113.42 - 120.30: 4197 120.30 - 127.17: 4668 127.17 - 134.04: 120 Bond angle restraints: 15417 Sorted by residual: angle pdb=" O13 POV A1203 " pdb=" P POV A1203 " pdb=" O14 POV A1203 " ideal model delta sigma weight residual 121.11 109.78 11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" OG1 THR A1152 " pdb=" CB THR A1152 " pdb=" CG2 THR A1152 " ideal model delta sigma weight residual 109.30 103.31 5.99 2.00e+00 2.50e-01 8.96e+00 angle pdb=" O11 POV A1203 " pdb=" P POV A1203 " pdb=" O12 POV A1203 " ideal model delta sigma weight residual 97.67 106.62 -8.95 3.00e+00 1.11e-01 8.89e+00 angle pdb=" C32 POV A1203 " pdb=" C31 POV A1203 " pdb=" O31 POV A1203 " ideal model delta sigma weight residual 110.66 119.24 -8.58 3.00e+00 1.11e-01 8.18e+00 angle pdb=" C22 POV A1203 " pdb=" C21 POV A1203 " pdb=" O21 POV A1203 " ideal model delta sigma weight residual 111.03 118.93 -7.90 3.00e+00 1.11e-01 6.93e+00 ... (remaining 15412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 6311 21.52 - 43.04: 446 43.04 - 64.55: 50 64.55 - 86.07: 20 86.07 - 107.59: 4 Dihedral angle restraints: 6831 sinusoidal: 2839 harmonic: 3992 Sorted by residual: dihedral pdb=" CB CYS B 91 " pdb=" SG CYS B 91 " pdb=" SG CYS B 104 " pdb=" CB CYS B 104 " ideal model delta sinusoidal sigma weight residual -86.00 -130.28 44.28 1 1.00e+01 1.00e-02 2.73e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.88 107.59 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C3 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 47.62 -58.01 105.63 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 6828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1466 0.054 - 0.108: 216 0.108 - 0.162: 41 0.162 - 0.216: 2 0.216 - 0.270: 1 Chirality restraints: 1726 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB THR A 432 " pdb=" CA THR A 432 " pdb=" OG1 THR A 432 " pdb=" CG2 THR A 432 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CB THR A1152 " pdb=" CA THR A1152 " pdb=" OG1 THR A1152 " pdb=" CG2 THR A1152 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 1723 not shown) Planarity restraints: 1941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 86 " 0.058 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO B 87 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 108 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO A 109 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 792 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO A 793 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 793 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 793 " 0.032 5.00e-02 4.00e+02 ... (remaining 1938 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 132 2.57 - 3.16: 9457 3.16 - 3.74: 17256 3.74 - 4.32: 25361 4.32 - 4.90: 42088 Nonbonded interactions: 94294 Sorted by model distance: nonbonded pdb=" OD2 ASP A 454 " pdb=" O3 VN4 A1201 " model vdw 1.992 3.040 nonbonded pdb=" OH TYR A1055 " pdb=" OG1 THR A1075 " model vdw 1.996 2.440 nonbonded pdb=" OD2 ASP A 454 " pdb="MG MG A1202 " model vdw 2.030 2.170 nonbonded pdb=" OG1 THR A 576 " pdb=" O TYR A 588 " model vdw 2.053 2.440 nonbonded pdb=" O HOH A1301 " pdb=" O HOH A1307 " model vdw 2.067 2.440 ... (remaining 94289 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=0.00 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: 0.810 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.080 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.580 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 0.072 11383 Z= 0.211 Angle : 0.577 11.332 15417 Z= 0.279 Chirality : 0.041 0.270 1726 Planarity : 0.005 0.087 1938 Dihedral : 14.734 107.591 4250 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.23), residues: 1349 helix: 0.14 (0.22), residues: 598 sheet: -0.22 (0.38), residues: 198 loop : -0.71 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 983 HIS 0.003 0.001 HIS B 283 PHE 0.016 0.001 PHE A 507 TYR 0.011 0.001 TYR B 122 ARG 0.010 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.340 Fit side-chains REVERT: A 538 MET cc_start: 0.8273 (mtm) cc_final: 0.7725 (mtp) REVERT: A 608 ARG cc_start: 0.7438 (ttt90) cc_final: 0.7079 (ttm-80) REVERT: B 215 ARG cc_start: 0.7462 (mtm110) cc_final: 0.7018 (mtm110) outliers start: 0 outliers final: 1 residues processed: 143 average time/residue: 1.0964 time to fit residues: 171.6285 Evaluate side-chains 107 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 105 optimal weight: 0.4980 chunk 40 optimal weight: 0.0670 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 549 GLN B 211 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11383 Z= 0.233 Angle : 0.581 10.308 15417 Z= 0.296 Chirality : 0.043 0.252 1726 Planarity : 0.005 0.066 1938 Dihedral : 8.561 73.483 1636 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.34 % Allowed : 9.02 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1349 helix: 0.72 (0.21), residues: 605 sheet: 0.05 (0.37), residues: 210 loop : -0.63 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 260 HIS 0.004 0.001 HIS B 283 PHE 0.027 0.001 PHE A 666 TYR 0.018 0.002 TYR B 273 ARG 0.007 0.001 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.6396 (tmm) cc_final: 0.6100 (tmm) REVERT: A 538 MET cc_start: 0.8266 (mtm) cc_final: 0.7861 (mtp) REVERT: A 608 ARG cc_start: 0.7735 (ttt90) cc_final: 0.7198 (ttm-80) REVERT: A 851 LYS cc_start: 0.7502 (tptt) cc_final: 0.7273 (tmtt) REVERT: A 1055 TYR cc_start: 0.6949 (m-80) cc_final: 0.6412 (m-80) REVERT: A 1179 GLN cc_start: 0.5684 (OUTLIER) cc_final: 0.4787 (mm110) REVERT: B 121 TYR cc_start: 0.8463 (m-80) cc_final: 0.8239 (m-80) REVERT: B 211 ASN cc_start: 0.8287 (m110) cc_final: 0.8025 (m-40) REVERT: B 261 MET cc_start: 0.8752 (mmm) cc_final: 0.8550 (mmm) outliers start: 16 outliers final: 9 residues processed: 120 average time/residue: 0.9738 time to fit residues: 129.5105 Evaluate side-chains 116 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 0.0170 chunk 102 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 109 optimal weight: 0.0010 chunk 121 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 98 optimal weight: 0.0670 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 442 ASN A 447 GLN A 872 GLN A1057 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11383 Z= 0.155 Angle : 0.512 11.060 15417 Z= 0.259 Chirality : 0.041 0.254 1726 Planarity : 0.004 0.057 1938 Dihedral : 7.368 74.872 1632 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.09 % Allowed : 10.44 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1349 helix: 0.92 (0.22), residues: 614 sheet: 0.34 (0.39), residues: 199 loop : -0.65 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 260 HIS 0.003 0.001 HIS B 283 PHE 0.018 0.001 PHE A 666 TYR 0.013 0.001 TYR B 273 ARG 0.005 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 1.252 Fit side-chains REVERT: A 95 ASN cc_start: 0.7691 (t0) cc_final: 0.7030 (t0) REVERT: A 107 PHE cc_start: 0.6831 (t80) cc_final: 0.6614 (t80) REVERT: A 110 MET cc_start: 0.6370 (OUTLIER) cc_final: 0.6036 (tmm) REVERT: A 289 ASP cc_start: 0.7237 (m-30) cc_final: 0.6963 (m-30) REVERT: A 479 HIS cc_start: 0.7412 (m-70) cc_final: 0.6825 (m90) REVERT: A 538 MET cc_start: 0.8118 (mtm) cc_final: 0.7914 (mtp) REVERT: A 608 ARG cc_start: 0.7863 (ttt90) cc_final: 0.7289 (ttm-80) REVERT: A 615 LYS cc_start: 0.5253 (mmtp) cc_final: 0.4912 (mmmm) REVERT: A 641 ASP cc_start: 0.8187 (m-30) cc_final: 0.7742 (m-30) REVERT: A 851 LYS cc_start: 0.7367 (tptt) cc_final: 0.7124 (tmtt) REVERT: A 898 VAL cc_start: 0.8196 (t) cc_final: 0.7907 (p) REVERT: A 1029 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.7469 (m-40) REVERT: A 1055 TYR cc_start: 0.6966 (m-80) cc_final: 0.6370 (m-80) REVERT: A 1179 GLN cc_start: 0.5652 (OUTLIER) cc_final: 0.4811 (mm110) REVERT: B 211 ASN cc_start: 0.8259 (m110) cc_final: 0.8046 (m110) outliers start: 25 outliers final: 7 residues processed: 144 average time/residue: 0.9445 time to fit residues: 150.8307 Evaluate side-chains 122 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 442 ASN A 474 GLN A1023 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11383 Z= 0.190 Angle : 0.539 14.881 15417 Z= 0.267 Chirality : 0.041 0.263 1726 Planarity : 0.004 0.054 1938 Dihedral : 7.102 79.530 1632 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.09 % Allowed : 12.20 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1349 helix: 0.97 (0.22), residues: 615 sheet: 0.24 (0.38), residues: 199 loop : -0.64 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.003 0.001 HIS B 283 PHE 0.025 0.001 PHE A 666 TYR 0.012 0.001 TYR B 121 ARG 0.008 0.000 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.263 Fit side-chains REVERT: A 95 ASN cc_start: 0.7717 (t0) cc_final: 0.7050 (t0) REVERT: A 110 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.6043 (tmm) REVERT: A 289 ASP cc_start: 0.7263 (m-30) cc_final: 0.6988 (m-30) REVERT: A 479 HIS cc_start: 0.7446 (m-70) cc_final: 0.6845 (m90) REVERT: A 538 MET cc_start: 0.8221 (mtm) cc_final: 0.7997 (mtp) REVERT: A 608 ARG cc_start: 0.7864 (ttt90) cc_final: 0.7293 (ttm-80) REVERT: A 615 LYS cc_start: 0.5316 (mmtp) cc_final: 0.4888 (mppt) REVERT: A 641 ASP cc_start: 0.8146 (m-30) cc_final: 0.7700 (m-30) REVERT: A 845 LYS cc_start: 0.7866 (mppt) cc_final: 0.7523 (mppt) REVERT: A 851 LYS cc_start: 0.7504 (tptt) cc_final: 0.7282 (tmtt) REVERT: A 898 VAL cc_start: 0.8218 (t) cc_final: 0.7933 (p) REVERT: A 1055 TYR cc_start: 0.6959 (m-80) cc_final: 0.6375 (m-80) REVERT: A 1179 GLN cc_start: 0.5691 (OUTLIER) cc_final: 0.4843 (mm110) REVERT: B 188 ILE cc_start: 0.6939 (mm) cc_final: 0.6712 (mt) REVERT: B 211 ASN cc_start: 0.8230 (m110) cc_final: 0.8012 (m110) outliers start: 25 outliers final: 10 residues processed: 131 average time/residue: 0.8797 time to fit residues: 129.0996 Evaluate side-chains 120 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 442 ASN A 479 HIS A 872 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11383 Z= 0.267 Angle : 0.565 12.117 15417 Z= 0.281 Chirality : 0.043 0.258 1726 Planarity : 0.004 0.053 1938 Dihedral : 7.195 82.516 1632 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.34 % Allowed : 14.20 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1349 helix: 0.83 (0.21), residues: 618 sheet: 0.18 (0.38), residues: 199 loop : -0.68 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.003 0.001 HIS B 283 PHE 0.019 0.002 PHE A 666 TYR 0.014 0.002 TYR B 122 ARG 0.006 0.000 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 0.985 Fit side-chains REVERT: A 95 ASN cc_start: 0.7789 (t0) cc_final: 0.7146 (t0) REVERT: A 110 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.6094 (tmm) REVERT: A 289 ASP cc_start: 0.7296 (m-30) cc_final: 0.7034 (m-30) REVERT: A 479 HIS cc_start: 0.7265 (m90) cc_final: 0.6708 (m90) REVERT: A 538 MET cc_start: 0.8269 (mtm) cc_final: 0.8011 (mtp) REVERT: A 608 ARG cc_start: 0.7872 (ttt90) cc_final: 0.7288 (ttm-80) REVERT: A 615 LYS cc_start: 0.5284 (mmtp) cc_final: 0.4760 (mppt) REVERT: A 845 LYS cc_start: 0.7786 (mppt) cc_final: 0.7454 (mppt) REVERT: A 851 LYS cc_start: 0.7650 (tptt) cc_final: 0.7103 (tptp) REVERT: A 898 VAL cc_start: 0.8243 (t) cc_final: 0.7954 (p) REVERT: A 1055 TYR cc_start: 0.7029 (m-80) cc_final: 0.6434 (m-80) REVERT: A 1179 GLN cc_start: 0.5654 (OUTLIER) cc_final: 0.4792 (mm110) REVERT: B 188 ILE cc_start: 0.7065 (mm) cc_final: 0.6850 (mt) REVERT: B 211 ASN cc_start: 0.8253 (m110) cc_final: 0.8035 (m110) outliers start: 28 outliers final: 13 residues processed: 126 average time/residue: 0.9287 time to fit residues: 129.8936 Evaluate side-chains 123 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 442 ASN A 474 GLN A 872 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11383 Z= 0.253 Angle : 0.559 12.080 15417 Z= 0.279 Chirality : 0.043 0.257 1726 Planarity : 0.004 0.050 1938 Dihedral : 7.067 82.657 1632 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.09 % Allowed : 15.54 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1349 helix: 0.88 (0.22), residues: 612 sheet: 0.13 (0.38), residues: 199 loop : -0.67 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1171 HIS 0.002 0.001 HIS B 283 PHE 0.016 0.001 PHE A 666 TYR 0.015 0.001 TYR A 405 ARG 0.006 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 95 ASN cc_start: 0.7764 (t0) cc_final: 0.7126 (t0) REVERT: A 110 MET cc_start: 0.6502 (OUTLIER) cc_final: 0.6082 (tmm) REVERT: A 289 ASP cc_start: 0.7263 (m-30) cc_final: 0.7017 (m-30) REVERT: A 479 HIS cc_start: 0.7270 (m90) cc_final: 0.6732 (m90) REVERT: A 538 MET cc_start: 0.8292 (mtm) cc_final: 0.8021 (mtp) REVERT: A 608 ARG cc_start: 0.7823 (ttt90) cc_final: 0.7464 (ttm-80) REVERT: A 615 LYS cc_start: 0.5223 (mmtp) cc_final: 0.4917 (mppt) REVERT: A 845 LYS cc_start: 0.7777 (mppt) cc_final: 0.7447 (mppt) REVERT: A 851 LYS cc_start: 0.7679 (tptt) cc_final: 0.7141 (tptp) REVERT: A 898 VAL cc_start: 0.8237 (t) cc_final: 0.7949 (p) REVERT: A 1179 GLN cc_start: 0.5731 (OUTLIER) cc_final: 0.4857 (mm110) REVERT: B 188 ILE cc_start: 0.7097 (mm) cc_final: 0.6887 (mt) REVERT: B 211 ASN cc_start: 0.8249 (m110) cc_final: 0.8031 (m110) outliers start: 25 outliers final: 14 residues processed: 128 average time/residue: 0.9229 time to fit residues: 132.0864 Evaluate side-chains 121 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 109 optimal weight: 0.4980 chunk 72 optimal weight: 0.5980 chunk 130 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 442 ASN A 474 GLN A1057 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11383 Z= 0.173 Angle : 0.531 12.332 15417 Z= 0.264 Chirality : 0.041 0.258 1726 Planarity : 0.004 0.049 1938 Dihedral : 6.742 82.079 1632 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.84 % Allowed : 16.37 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.24), residues: 1349 helix: 1.05 (0.22), residues: 610 sheet: 0.22 (0.39), residues: 199 loop : -0.65 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 260 HIS 0.003 0.001 HIS A 359 PHE 0.014 0.001 PHE A 666 TYR 0.014 0.001 TYR A 405 ARG 0.006 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: A 95 ASN cc_start: 0.7685 (t0) cc_final: 0.7027 (t0) REVERT: A 110 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.6050 (tmm) REVERT: A 289 ASP cc_start: 0.7184 (m-30) cc_final: 0.6931 (m-30) REVERT: A 479 HIS cc_start: 0.7255 (m90) cc_final: 0.6702 (m90) REVERT: A 538 MET cc_start: 0.8271 (mtm) cc_final: 0.7984 (mtp) REVERT: A 608 ARG cc_start: 0.7822 (ttt90) cc_final: 0.7457 (ttm-80) REVERT: A 845 LYS cc_start: 0.7798 (mppt) cc_final: 0.7457 (mppt) REVERT: A 851 LYS cc_start: 0.7636 (tptt) cc_final: 0.7103 (tptp) REVERT: A 898 VAL cc_start: 0.8208 (t) cc_final: 0.7933 (p) REVERT: A 1179 GLN cc_start: 0.5696 (OUTLIER) cc_final: 0.4860 (mm110) REVERT: B 188 ILE cc_start: 0.7037 (mm) cc_final: 0.6833 (mt) REVERT: B 211 ASN cc_start: 0.8224 (m110) cc_final: 0.7997 (m110) outliers start: 22 outliers final: 16 residues processed: 127 average time/residue: 0.9001 time to fit residues: 127.7376 Evaluate side-chains 122 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 118 optimal weight: 0.3980 chunk 124 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11383 Z= 0.265 Angle : 0.566 12.550 15417 Z= 0.282 Chirality : 0.043 0.258 1726 Planarity : 0.004 0.048 1938 Dihedral : 6.818 83.565 1632 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.42 % Allowed : 17.13 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1349 helix: 1.03 (0.22), residues: 604 sheet: 0.14 (0.38), residues: 199 loop : -0.62 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1171 HIS 0.002 0.001 HIS B 283 PHE 0.023 0.001 PHE A1097 TYR 0.015 0.002 TYR A 405 ARG 0.005 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 95 ASN cc_start: 0.7726 (t0) cc_final: 0.7093 (t0) REVERT: A 110 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.6107 (tmm) REVERT: A 241 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.6754 (tpt) REVERT: A 289 ASP cc_start: 0.7208 (m-30) cc_final: 0.6957 (m-30) REVERT: A 479 HIS cc_start: 0.7306 (m90) cc_final: 0.6761 (m90) REVERT: A 538 MET cc_start: 0.8331 (mtm) cc_final: 0.8062 (mtp) REVERT: A 608 ARG cc_start: 0.7816 (ttt90) cc_final: 0.7450 (ttm-80) REVERT: A 845 LYS cc_start: 0.7801 (mppt) cc_final: 0.7463 (mppt) REVERT: A 851 LYS cc_start: 0.7670 (tptt) cc_final: 0.7153 (tptp) REVERT: A 898 VAL cc_start: 0.8249 (t) cc_final: 0.7953 (p) REVERT: A 1000 MET cc_start: 0.7848 (tmm) cc_final: 0.7623 (ttt) REVERT: A 1179 GLN cc_start: 0.5778 (OUTLIER) cc_final: 0.4951 (mm110) REVERT: B 51 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6793 (mp) REVERT: B 211 ASN cc_start: 0.8211 (m110) cc_final: 0.7986 (m110) REVERT: B 261 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8234 (mmm) outliers start: 29 outliers final: 19 residues processed: 126 average time/residue: 0.9213 time to fit residues: 130.1949 Evaluate side-chains 127 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 124 optimal weight: 0.0070 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.0970 chunk 95 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 109 optimal weight: 0.0980 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11383 Z= 0.147 Angle : 0.531 12.834 15417 Z= 0.262 Chirality : 0.040 0.259 1726 Planarity : 0.004 0.049 1938 Dihedral : 6.435 80.982 1632 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.09 % Allowed : 17.79 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1349 helix: 1.16 (0.22), residues: 613 sheet: 0.30 (0.39), residues: 198 loop : -0.67 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1171 HIS 0.005 0.001 HIS A 359 PHE 0.026 0.001 PHE A 666 TYR 0.012 0.001 TYR A 405 ARG 0.007 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASN cc_start: 0.7603 (t0) cc_final: 0.6946 (t0) REVERT: A 110 MET cc_start: 0.6353 (OUTLIER) cc_final: 0.6077 (tmm) REVERT: A 241 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.6734 (tpt) REVERT: A 289 ASP cc_start: 0.7181 (m-30) cc_final: 0.6928 (m-30) REVERT: A 479 HIS cc_start: 0.7365 (m90) cc_final: 0.6811 (m90) REVERT: A 538 MET cc_start: 0.8305 (mtm) cc_final: 0.8081 (mtp) REVERT: A 608 ARG cc_start: 0.7867 (ttt90) cc_final: 0.7488 (ttm-80) REVERT: A 845 LYS cc_start: 0.7787 (mppt) cc_final: 0.7447 (mppt) REVERT: A 851 LYS cc_start: 0.7620 (tptt) cc_final: 0.7076 (tptp) REVERT: A 898 VAL cc_start: 0.8195 (t) cc_final: 0.7918 (p) REVERT: A 1000 MET cc_start: 0.7675 (tmm) cc_final: 0.7456 (ttt) REVERT: A 1179 GLN cc_start: 0.5681 (OUTLIER) cc_final: 0.4819 (mm110) REVERT: B 51 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6904 (mp) REVERT: B 211 ASN cc_start: 0.8165 (m110) cc_final: 0.7960 (m110) outliers start: 25 outliers final: 16 residues processed: 125 average time/residue: 0.8648 time to fit residues: 120.8354 Evaluate side-chains 122 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 0.0570 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11383 Z= 0.181 Angle : 0.551 12.947 15417 Z= 0.271 Chirality : 0.041 0.259 1726 Planarity : 0.004 0.052 1938 Dihedral : 6.411 82.320 1632 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.75 % Allowed : 18.46 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1349 helix: 1.15 (0.22), residues: 613 sheet: 0.31 (0.39), residues: 199 loop : -0.66 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1171 HIS 0.003 0.001 HIS A 359 PHE 0.023 0.001 PHE A 529 TYR 0.012 0.001 TYR A 405 ARG 0.005 0.000 ARG A 628 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7903 (ptpt) cc_final: 0.7265 (pptt) REVERT: A 95 ASN cc_start: 0.7622 (t0) cc_final: 0.7012 (t0) REVERT: A 110 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.6254 (tmm) REVERT: A 241 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.6737 (tpt) REVERT: A 289 ASP cc_start: 0.7155 (m-30) cc_final: 0.6896 (m-30) REVERT: A 608 ARG cc_start: 0.7868 (ttt90) cc_final: 0.7565 (ttm-80) REVERT: A 845 LYS cc_start: 0.7792 (mppt) cc_final: 0.7453 (mppt) REVERT: A 851 LYS cc_start: 0.7633 (tptt) cc_final: 0.7094 (tptp) REVERT: A 898 VAL cc_start: 0.8218 (t) cc_final: 0.7936 (p) REVERT: A 1179 GLN cc_start: 0.5700 (OUTLIER) cc_final: 0.4841 (mm110) REVERT: B 51 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6886 (mp) REVERT: B 211 ASN cc_start: 0.8157 (m110) cc_final: 0.7948 (m110) outliers start: 21 outliers final: 17 residues processed: 120 average time/residue: 0.9223 time to fit residues: 123.5496 Evaluate side-chains 124 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 110 optimal weight: 0.0470 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** 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 = 0.4151 r_free = 0.4151 target = 0.175694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126732 restraints weight = 12462.466| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.34 r_work: 0.3450 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11383 Z= 0.166 Angle : 0.552 12.975 15417 Z= 0.272 Chirality : 0.041 0.259 1726 Planarity : 0.004 0.052 1938 Dihedral : 6.326 82.851 1632 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.01 % Allowed : 18.46 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.24), residues: 1349 helix: 1.18 (0.22), residues: 612 sheet: 0.34 (0.39), residues: 200 loop : -0.68 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1171 HIS 0.004 0.001 HIS A 359 PHE 0.023 0.001 PHE A 529 TYR 0.012 0.001 TYR A 405 ARG 0.005 0.000 ARG A 628 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3189.76 seconds wall clock time: 57 minutes 42.57 seconds (3462.57 seconds total)