Starting phenix.real_space_refine on Tue Sep 24 03:53:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qla_14066/09_2024/7qla_14066.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qla_14066/09_2024/7qla_14066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qla_14066/09_2024/7qla_14066.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qla_14066/09_2024/7qla_14066.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qla_14066/09_2024/7qla_14066.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qla_14066/09_2024/7qla_14066.cif" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 21 5.16 5 C 4372 2.51 5 N 1187 2.21 5 O 1257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6837 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3377 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 411} Chain breaks: 2 Chain: "C" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3460 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 416} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.32, per 1000 atoms: 0.63 Number of scatterers: 6837 At special positions: 0 Unit cell: (81.75, 103.55, 110.09, 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 21 16.00 O 1257 8.00 N 1187 7.00 C 4372 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 974.6 milliseconds 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 43.6% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.621A pdb=" N LEU A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 removed outlier: 3.501A pdb=" N ALA A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 262 removed outlier: 4.147A pdb=" N SER A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 314 Processing helix chain 'A' and resid 315 through 323 removed outlier: 3.760A pdb=" N ASN A 321 " --> pdb=" O PRO A 317 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 352 Processing helix chain 'A' and resid 353 through 359 removed outlier: 3.515A pdb=" N LEU A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.959A pdb=" N SER A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 removed outlier: 3.562A pdb=" N LEU A 413 " --> pdb=" O HIS A 409 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 416 " --> pdb=" O ASP A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 499 through 518 removed outlier: 3.573A pdb=" N SER A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 513 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 529 removed outlier: 3.670A pdb=" N SER A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 570 through 593 removed outlier: 3.764A pdb=" N THR A 574 " --> pdb=" O THR A 570 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU A 588 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 590 " --> pdb=" O GLU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 653 removed outlier: 5.417A pdb=" N GLU A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ARG A 645 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN A 648 " --> pdb=" O ASN A 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.793A pdb=" N GLU C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 removed outlier: 3.987A pdb=" N GLN C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 120 removed outlier: 3.722A pdb=" N ILE C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C 108 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE C 118 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 209 removed outlier: 3.842A pdb=" N LEU C 196 " --> pdb=" O PRO C 192 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG C 197 " --> pdb=" O PRO C 193 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 240 removed outlier: 3.627A pdb=" N ALA C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ARG C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ALA C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN C 226 " --> pdb=" O GLN C 222 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 255 removed outlier: 4.214A pdb=" N PHE C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 290 removed outlier: 3.807A pdb=" N VAL C 282 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU C 288 " --> pdb=" O GLU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 354 removed outlier: 4.217A pdb=" N GLY C 343 " --> pdb=" O LYS C 339 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 345 " --> pdb=" O LEU C 341 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 351 " --> pdb=" O TRP C 347 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR C 352 " --> pdb=" O MET C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 555 No H-bonds generated for 'chain 'C' and resid 553 through 555' Processing helix chain 'C' and resid 556 through 568 removed outlier: 3.520A pdb=" N LEU C 560 " --> pdb=" O THR C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 572 through 580 removed outlier: 3.541A pdb=" N HIS C 577 " --> pdb=" O LYS C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 667 removed outlier: 3.597A pdb=" N ALA C 652 " --> pdb=" O THR C 648 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 653 " --> pdb=" O ARG C 649 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN C 654 " --> pdb=" O VAL C 650 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 660 " --> pdb=" O HIS C 656 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 663 " --> pdb=" O ILE C 659 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 237 removed outlier: 6.385A pdb=" N ILE A 227 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER A 237 " --> pdb=" O TYR A 225 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TYR A 225 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 281 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 396 through 401 removed outlier: 6.706A pdb=" N LEU A 391 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL A 400 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLY A 389 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 558 removed outlier: 3.985A pdb=" N GLN A 555 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER A 550 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS A 545 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 629 " --> pdb=" O HIS A 545 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 615 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 555 through 558 removed outlier: 3.985A pdb=" N GLN A 555 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER A 550 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS A 545 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 629 " --> pdb=" O HIS A 545 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 626 " --> pdb=" O TRP A 619 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 38 through 41 removed outlier: 6.504A pdb=" N ILE C 22 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR C 41 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU C 20 " --> pdb=" O TYR C 41 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU C 17 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASP C 150 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE C 19 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TRP C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 152 through 154 removed outlier: 3.557A pdb=" N SER C 186 " --> pdb=" O THR C 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 258 through 260 removed outlier: 5.439A pdb=" N ILE C 258 " --> pdb=" O LEU C 614 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER C 616 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU C 260 " --> pdb=" O SER C 616 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR C 613 " --> pdb=" O ASP C 608 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 605 " --> pdb=" O HIS C 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 328 through 329 removed outlier: 4.017A pdb=" N ASP C 295 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 297 " --> pdb=" O ILE C 544 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 299 " --> pdb=" O ILE C 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 601 through 603 removed outlier: 3.915A pdb=" N GLN C 601 " --> pdb=" O VAL C 736 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 849 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: 1.81 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2227 1.34 - 1.46: 986 1.46 - 1.57: 3738 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 6983 Sorted by residual: bond pdb=" N ASN A 444 " pdb=" CA ASN A 444 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.90e+00 bond pdb=" CB GLN C 314 " pdb=" CG GLN C 314 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.32e-01 bond pdb=" CB LYS C 95 " pdb=" CG LYS C 95 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.77e-01 bond pdb=" C PRO A 566 " pdb=" N PRO A 567 " ideal model delta sigma weight residual 1.335 1.345 -0.011 1.28e-02 6.10e+03 6.91e-01 bond pdb=" CA ASN A 444 " pdb=" CB ASN A 444 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.78e-01 ... (remaining 6978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 9088 1.37 - 2.73: 290 2.73 - 4.10: 66 4.10 - 5.47: 16 5.47 - 6.84: 7 Bond angle restraints: 9467 Sorted by residual: angle pdb=" C ASN A 443 " pdb=" N ASN A 444 " pdb=" CA ASN A 444 " ideal model delta sigma weight residual 121.54 127.48 -5.94 1.91e+00 2.74e-01 9.68e+00 angle pdb=" CB LYS C 95 " pdb=" CG LYS C 95 " pdb=" CD LYS C 95 " ideal model delta sigma weight residual 111.30 117.23 -5.93 2.30e+00 1.89e-01 6.66e+00 angle pdb=" CB ARG A 595 " pdb=" CG ARG A 595 " pdb=" CD ARG A 595 " ideal model delta sigma weight residual 111.30 116.82 -5.52 2.30e+00 1.89e-01 5.76e+00 angle pdb=" CA ASN A 444 " pdb=" CB ASN A 444 " pdb=" CG ASN A 444 " ideal model delta sigma weight residual 112.60 114.96 -2.36 1.00e+00 1.00e+00 5.56e+00 angle pdb=" CG1 ILE A 426 " pdb=" CB ILE A 426 " pdb=" CG2 ILE A 426 " ideal model delta sigma weight residual 110.70 103.86 6.84 3.00e+00 1.11e-01 5.19e+00 ... (remaining 9462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 3736 17.33 - 34.65: 347 34.65 - 51.98: 63 51.98 - 69.31: 9 69.31 - 86.63: 6 Dihedral angle restraints: 4161 sinusoidal: 1671 harmonic: 2490 Sorted by residual: dihedral pdb=" CA LEU A 387 " pdb=" C LEU A 387 " pdb=" N TYR A 388 " pdb=" CA TYR A 388 " ideal model delta harmonic sigma weight residual 180.00 155.63 24.37 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA VAL C 537 " pdb=" C VAL C 537 " pdb=" N SER C 538 " pdb=" CA SER C 538 " ideal model delta harmonic sigma weight residual 180.00 156.58 23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA GLN C 539 " pdb=" C GLN C 539 " pdb=" N PRO C 540 " pdb=" CA PRO C 540 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 4158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 771 0.039 - 0.078: 214 0.078 - 0.116: 75 0.116 - 0.155: 13 0.155 - 0.194: 3 Chirality restraints: 1076 Sorted by residual: chirality pdb=" CB ILE A 426 " pdb=" CA ILE A 426 " pdb=" CG1 ILE A 426 " pdb=" CG2 ILE A 426 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CA THR C 551 " pdb=" N THR C 551 " pdb=" C THR C 551 " pdb=" CB THR C 551 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CA ASN A 444 " pdb=" N ASN A 444 " pdb=" C ASN A 444 " pdb=" CB ASN A 444 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 1073 not shown) Planarity restraints: 1200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 443 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C ASN A 443 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN A 443 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN A 444 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 619 " 0.011 2.00e-02 2.50e+03 1.06e-02 2.82e+00 pdb=" CG TRP A 619 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 619 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 619 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 619 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 619 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 619 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 619 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 619 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 619 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 565 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A 566 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 566 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 566 " 0.022 5.00e-02 4.00e+02 ... (remaining 1197 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 124 2.67 - 3.23: 6740 3.23 - 3.79: 10424 3.79 - 4.34: 13660 4.34 - 4.90: 22403 Nonbonded interactions: 53351 Sorted by model distance: nonbonded pdb=" OH TYR C 183 " pdb=" OH TYR C 185 " model vdw 2.117 3.040 nonbonded pdb=" OG1 THR C 129 " pdb=" O ALA C 132 " model vdw 2.239 3.040 nonbonded pdb=" O ALA C 566 " pdb=" OG SER C 569 " model vdw 2.272 3.040 nonbonded pdb=" OE2 GLU C 651 " pdb=" OG1 THR C 655 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR A 225 " pdb=" OE1 GLN A 302 " model vdw 2.282 3.040 ... (remaining 53346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 0.290 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.840 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 0.031 6983 Z= 0.193 Angle : 0.616 6.837 9467 Z= 0.304 Chirality : 0.042 0.194 1076 Planarity : 0.004 0.048 1200 Dihedral : 13.830 86.631 2559 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.28), residues: 850 helix: 0.15 (0.29), residues: 313 sheet: -0.63 (0.42), residues: 153 loop : -1.84 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 619 HIS 0.016 0.001 HIS A 545 PHE 0.020 0.002 PHE C 114 TYR 0.017 0.001 TYR A 388 ARG 0.012 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LYS cc_start: 0.8445 (tptm) cc_final: 0.8219 (tptt) REVERT: A 249 MET cc_start: 0.8077 (tpp) cc_final: 0.7598 (tpp) REVERT: A 308 MET cc_start: 0.8469 (tpp) cc_final: 0.8136 (mmm) REVERT: A 559 SER cc_start: 0.8921 (p) cc_final: 0.8647 (p) REVERT: A 587 GLU cc_start: 0.7209 (mp0) cc_final: 0.6915 (mp0) REVERT: C 95 LYS cc_start: 0.8778 (tppt) cc_final: 0.8517 (tptt) REVERT: C 253 ASP cc_start: 0.8034 (m-30) cc_final: 0.7474 (m-30) REVERT: C 284 GLU cc_start: 0.7930 (tt0) cc_final: 0.7546 (tt0) REVERT: C 349 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7349 (mm-30) REVERT: C 659 ILE cc_start: 0.9393 (mt) cc_final: 0.9100 (mt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1795 time to fit residues: 39.9604 Evaluate side-chains 124 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 0.4980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6983 Z= 0.255 Angle : 0.688 7.240 9467 Z= 0.350 Chirality : 0.045 0.175 1076 Planarity : 0.005 0.039 1200 Dihedral : 4.833 24.451 948 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.03 % Allowed : 10.70 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.29), residues: 850 helix: 0.26 (0.28), residues: 343 sheet: -0.54 (0.44), residues: 150 loop : -1.60 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 647 HIS 0.007 0.001 HIS A 545 PHE 0.024 0.002 PHE A 258 TYR 0.022 0.002 TYR A 585 ARG 0.007 0.000 ARG C 582 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 LEU cc_start: 0.8515 (tt) cc_final: 0.8230 (tt) REVERT: A 404 ARG cc_start: 0.6929 (mmp-170) cc_final: 0.6587 (mmp-170) REVERT: A 524 ARG cc_start: 0.8420 (mpp80) cc_final: 0.7395 (mpt-90) REVERT: A 559 SER cc_start: 0.9020 (p) cc_final: 0.8789 (p) REVERT: A 586 GLU cc_start: 0.6502 (pt0) cc_final: 0.6262 (pt0) REVERT: A 587 GLU cc_start: 0.7511 (mp0) cc_final: 0.7119 (mp0) REVERT: A 619 TRP cc_start: 0.6863 (t60) cc_final: 0.6249 (t60) REVERT: C 40 TYR cc_start: 0.8576 (t80) cc_final: 0.8208 (t80) REVERT: C 222 GLN cc_start: 0.7694 (mm110) cc_final: 0.7486 (mm110) REVERT: C 253 ASP cc_start: 0.8042 (m-30) cc_final: 0.7464 (m-30) REVERT: C 349 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7242 (mm-30) REVERT: C 659 ILE cc_start: 0.9363 (mt) cc_final: 0.9131 (mt) outliers start: 15 outliers final: 12 residues processed: 146 average time/residue: 0.1876 time to fit residues: 36.4586 Evaluate side-chains 137 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 628 CYS Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 559 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6983 Z= 0.190 Angle : 0.639 8.671 9467 Z= 0.318 Chirality : 0.044 0.173 1076 Planarity : 0.004 0.043 1200 Dihedral : 4.748 24.237 948 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.12 % Allowed : 14.23 % Favored : 82.66 % 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: -0.91 (0.29), residues: 850 helix: 0.39 (0.28), residues: 347 sheet: -0.43 (0.43), residues: 150 loop : -1.65 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 647 HIS 0.007 0.001 HIS A 545 PHE 0.022 0.002 PHE C 234 TYR 0.026 0.002 TYR A 585 ARG 0.006 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.796 Fit side-chains REVERT: A 227 ILE cc_start: 0.7985 (mm) cc_final: 0.7767 (mt) REVERT: A 404 ARG cc_start: 0.6869 (mmp-170) cc_final: 0.6470 (mmp-170) REVERT: A 559 SER cc_start: 0.9047 (p) cc_final: 0.8773 (p) REVERT: A 582 MET cc_start: 0.7112 (mpp) cc_final: 0.6725 (mpp) REVERT: A 587 GLU cc_start: 0.7469 (mp0) cc_final: 0.7219 (mp0) REVERT: A 619 TRP cc_start: 0.7032 (OUTLIER) cc_final: 0.6625 (t60) REVERT: C 40 TYR cc_start: 0.8463 (t80) cc_final: 0.8067 (t80) REVERT: C 253 ASP cc_start: 0.8024 (m-30) cc_final: 0.7441 (m-30) REVERT: C 659 ILE cc_start: 0.9333 (mt) cc_final: 0.9086 (mt) outliers start: 23 outliers final: 17 residues processed: 137 average time/residue: 0.1785 time to fit residues: 33.0639 Evaluate side-chains 137 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 628 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 559 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 79 optimal weight: 0.0870 chunk 84 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 22 optimal weight: 0.0870 chunk 70 optimal weight: 0.0010 overall best weight: 1.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6983 Z= 0.241 Angle : 0.651 8.583 9467 Z= 0.327 Chirality : 0.044 0.156 1076 Planarity : 0.004 0.044 1200 Dihedral : 4.759 24.561 948 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.07 % Allowed : 15.72 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.29), residues: 850 helix: 0.48 (0.28), residues: 348 sheet: -0.54 (0.41), residues: 163 loop : -1.59 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 647 HIS 0.010 0.001 HIS A 545 PHE 0.021 0.002 PHE C 541 TYR 0.032 0.002 TYR A 585 ARG 0.004 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 227 ILE cc_start: 0.7997 (mm) cc_final: 0.7777 (mt) REVERT: A 249 MET cc_start: 0.8400 (tpp) cc_final: 0.8020 (tpp) REVERT: A 299 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.7989 (mm) REVERT: A 404 ARG cc_start: 0.6951 (mmp-170) cc_final: 0.6581 (mmp-170) REVERT: A 545 HIS cc_start: 0.7845 (m170) cc_final: 0.7630 (m170) REVERT: A 582 MET cc_start: 0.7162 (mpp) cc_final: 0.6759 (mpp) REVERT: A 587 GLU cc_start: 0.7571 (mp0) cc_final: 0.7331 (mp0) REVERT: A 619 TRP cc_start: 0.7149 (OUTLIER) cc_final: 0.6631 (t60) REVERT: C 40 TYR cc_start: 0.8542 (t80) cc_final: 0.8215 (t80) REVERT: C 253 ASP cc_start: 0.8066 (m-30) cc_final: 0.7463 (m-30) REVERT: C 659 ILE cc_start: 0.9336 (mt) cc_final: 0.9097 (mt) outliers start: 30 outliers final: 18 residues processed: 145 average time/residue: 0.1887 time to fit residues: 36.7040 Evaluate side-chains 143 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 628 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 559 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 9.9990 chunk 1 optimal weight: 0.0270 chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.0040 overall best weight: 1.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6983 Z= 0.240 Angle : 0.669 8.113 9467 Z= 0.333 Chirality : 0.045 0.180 1076 Planarity : 0.004 0.044 1200 Dihedral : 4.760 24.613 948 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.61 % Allowed : 17.21 % Favored : 78.18 % 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: -0.80 (0.29), residues: 850 helix: 0.51 (0.28), residues: 354 sheet: -0.65 (0.41), residues: 164 loop : -1.55 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 647 HIS 0.006 0.001 HIS A 545 PHE 0.019 0.002 PHE C 541 TYR 0.029 0.002 TYR A 585 ARG 0.011 0.001 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 0.870 Fit side-chains REVERT: A 299 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.7989 (mm) REVERT: A 404 ARG cc_start: 0.6947 (mmp-170) cc_final: 0.6631 (mmp-170) REVERT: A 582 MET cc_start: 0.7188 (mpp) cc_final: 0.6851 (mpp) REVERT: A 619 TRP cc_start: 0.7147 (OUTLIER) cc_final: 0.6635 (t60) REVERT: C 40 TYR cc_start: 0.8511 (t80) cc_final: 0.8116 (t80) REVERT: C 222 GLN cc_start: 0.7781 (mm110) cc_final: 0.7453 (mm110) REVERT: C 253 ASP cc_start: 0.7956 (m-30) cc_final: 0.7348 (m-30) REVERT: C 659 ILE cc_start: 0.9328 (mt) cc_final: 0.9082 (mt) outliers start: 34 outliers final: 21 residues processed: 149 average time/residue: 0.1792 time to fit residues: 35.7751 Evaluate side-chains 147 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 628 CYS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 559 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN A 376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6983 Z= 0.263 Angle : 0.688 7.715 9467 Z= 0.339 Chirality : 0.045 0.171 1076 Planarity : 0.004 0.044 1200 Dihedral : 4.767 24.982 948 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 5.01 % Allowed : 17.89 % Favored : 77.10 % 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: -0.82 (0.29), residues: 850 helix: 0.56 (0.28), residues: 354 sheet: -0.70 (0.40), residues: 164 loop : -1.61 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 647 HIS 0.003 0.001 HIS C 99 PHE 0.019 0.002 PHE C 541 TYR 0.028 0.002 TYR A 585 ARG 0.007 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 299 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.7947 (mm) REVERT: A 404 ARG cc_start: 0.6982 (mmp-170) cc_final: 0.6655 (mmp-170) REVERT: A 506 MET cc_start: 0.7402 (ttm) cc_final: 0.7057 (ttm) REVERT: A 524 ARG cc_start: 0.8347 (tpp80) cc_final: 0.7966 (mmm-85) REVERT: A 582 MET cc_start: 0.7216 (mpp) cc_final: 0.6906 (mpp) REVERT: A 619 TRP cc_start: 0.7214 (OUTLIER) cc_final: 0.6715 (t60) REVERT: C 40 TYR cc_start: 0.8496 (t80) cc_final: 0.8152 (t80) REVERT: C 47 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6358 (tt) REVERT: C 116 LYS cc_start: 0.8738 (ttpt) cc_final: 0.7931 (ttpt) REVERT: C 222 GLN cc_start: 0.7868 (mm110) cc_final: 0.7569 (mm110) REVERT: C 231 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7973 (mp) REVERT: C 253 ASP cc_start: 0.8033 (m-30) cc_final: 0.7423 (m-30) REVERT: C 338 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8533 (mmt90) REVERT: C 659 ILE cc_start: 0.9306 (mt) cc_final: 0.9064 (mt) outliers start: 37 outliers final: 24 residues processed: 153 average time/residue: 0.1921 time to fit residues: 39.5985 Evaluate side-chains 149 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 628 CYS Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 617 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 52 optimal weight: 0.2980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.0370 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6983 Z= 0.190 Angle : 0.673 8.701 9467 Z= 0.328 Chirality : 0.044 0.176 1076 Planarity : 0.004 0.043 1200 Dihedral : 4.638 24.142 948 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.07 % Allowed : 19.24 % Favored : 76.69 % 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: -0.72 (0.29), residues: 850 helix: 0.65 (0.28), residues: 354 sheet: -0.69 (0.40), residues: 165 loop : -1.55 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 647 HIS 0.004 0.001 HIS A 409 PHE 0.017 0.002 PHE C 234 TYR 0.031 0.002 TYR A 585 ARG 0.004 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 0.760 Fit side-chains REVERT: A 219 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8601 (tptt) REVERT: A 249 MET cc_start: 0.8368 (tpp) cc_final: 0.7983 (tpp) REVERT: A 299 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7832 (mm) REVERT: A 404 ARG cc_start: 0.6852 (mmp-170) cc_final: 0.6558 (mmp-170) REVERT: A 524 ARG cc_start: 0.8297 (tpp80) cc_final: 0.7954 (mmm-85) REVERT: A 582 MET cc_start: 0.7351 (mpp) cc_final: 0.6495 (mmm) REVERT: A 619 TRP cc_start: 0.6983 (OUTLIER) cc_final: 0.6504 (t60) REVERT: C 40 TYR cc_start: 0.8319 (t80) cc_final: 0.7886 (t80) REVERT: C 222 GLN cc_start: 0.7811 (mm110) cc_final: 0.7593 (mm110) REVERT: C 253 ASP cc_start: 0.7937 (m-30) cc_final: 0.7340 (m-30) REVERT: C 659 ILE cc_start: 0.9306 (mt) cc_final: 0.9061 (mt) outliers start: 30 outliers final: 22 residues processed: 148 average time/residue: 0.1866 time to fit residues: 37.3632 Evaluate side-chains 147 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 617 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6983 Z= 0.296 Angle : 0.725 7.829 9467 Z= 0.358 Chirality : 0.046 0.184 1076 Planarity : 0.005 0.045 1200 Dihedral : 4.805 24.900 948 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.74 % Allowed : 18.97 % Favored : 76.29 % 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: -0.81 (0.29), residues: 850 helix: 0.64 (0.28), residues: 349 sheet: -0.79 (0.40), residues: 164 loop : -1.61 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 647 HIS 0.004 0.001 HIS C 99 PHE 0.024 0.002 PHE C 541 TYR 0.029 0.002 TYR A 585 ARG 0.010 0.001 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 219 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8618 (tptt) REVERT: A 249 MET cc_start: 0.8374 (tpp) cc_final: 0.8139 (tpp) REVERT: A 299 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.7991 (mm) REVERT: A 404 ARG cc_start: 0.6992 (mmp-170) cc_final: 0.6668 (mmp-170) REVERT: A 506 MET cc_start: 0.7365 (ttm) cc_final: 0.7113 (ttm) REVERT: A 524 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7967 (mmm-85) REVERT: A 573 GLU cc_start: 0.8084 (pm20) cc_final: 0.7866 (pm20) REVERT: A 582 MET cc_start: 0.7156 (mpp) cc_final: 0.6444 (mmm) REVERT: A 619 TRP cc_start: 0.7114 (OUTLIER) cc_final: 0.6611 (t60) REVERT: C 40 TYR cc_start: 0.8537 (t80) cc_final: 0.8216 (t80) REVERT: C 47 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6419 (tt) REVERT: C 116 LYS cc_start: 0.8563 (ttpt) cc_final: 0.7981 (ttpt) REVERT: C 222 GLN cc_start: 0.7873 (mm110) cc_final: 0.7623 (mm110) REVERT: C 231 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7933 (mp) REVERT: C 253 ASP cc_start: 0.7987 (m-30) cc_final: 0.7362 (m-30) REVERT: C 471 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7434 (t80) REVERT: C 659 ILE cc_start: 0.9304 (mt) cc_final: 0.9059 (mt) outliers start: 35 outliers final: 25 residues processed: 146 average time/residue: 0.1794 time to fit residues: 35.4123 Evaluate side-chains 155 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 628 CYS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 617 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 0.0170 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6983 Z= 0.200 Angle : 0.701 8.134 9467 Z= 0.344 Chirality : 0.044 0.181 1076 Planarity : 0.004 0.042 1200 Dihedral : 4.667 23.864 948 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.93 % Allowed : 20.19 % Favored : 75.88 % 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: -0.69 (0.29), residues: 850 helix: 0.70 (0.29), residues: 349 sheet: -0.53 (0.41), residues: 158 loop : -1.61 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 647 HIS 0.004 0.000 HIS C 99 PHE 0.018 0.002 PHE C 234 TYR 0.024 0.002 TYR A 585 ARG 0.007 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 219 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8573 (tptt) REVERT: A 249 MET cc_start: 0.8350 (tpp) cc_final: 0.7978 (tpp) REVERT: A 299 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7836 (mm) REVERT: A 404 ARG cc_start: 0.6850 (mmp-170) cc_final: 0.6554 (mmp-170) REVERT: A 506 MET cc_start: 0.7275 (ttm) cc_final: 0.7035 (ttm) REVERT: A 582 MET cc_start: 0.7400 (mpp) cc_final: 0.6306 (mmm) REVERT: A 619 TRP cc_start: 0.7116 (OUTLIER) cc_final: 0.6581 (t60) REVERT: C 40 TYR cc_start: 0.8354 (t80) cc_final: 0.7950 (t80) REVERT: C 116 LYS cc_start: 0.8478 (ttpt) cc_final: 0.7891 (ttpt) REVERT: C 253 ASP cc_start: 0.7957 (m-30) cc_final: 0.7315 (m-30) REVERT: C 471 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.6788 (t80) REVERT: C 577 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.7731 (t-90) REVERT: C 659 ILE cc_start: 0.9314 (mt) cc_final: 0.9067 (mt) outliers start: 29 outliers final: 22 residues processed: 148 average time/residue: 0.1756 time to fit residues: 35.3055 Evaluate side-chains 141 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 577 HIS Chi-restraints excluded: chain C residue 617 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 7 optimal weight: 0.0170 chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6983 Z= 0.288 Angle : 0.739 7.990 9467 Z= 0.367 Chirality : 0.046 0.178 1076 Planarity : 0.005 0.045 1200 Dihedral : 4.803 24.983 948 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.07 % Allowed : 21.27 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.29), residues: 850 helix: 0.61 (0.29), residues: 349 sheet: -0.76 (0.39), residues: 164 loop : -1.63 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 647 HIS 0.004 0.001 HIS C 99 PHE 0.028 0.002 PHE C 238 TYR 0.031 0.002 TYR A 585 ARG 0.009 0.001 ARG A 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 219 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8632 (tptt) REVERT: A 249 MET cc_start: 0.8355 (tpp) cc_final: 0.8128 (tpp) REVERT: A 299 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.7934 (mm) REVERT: A 404 ARG cc_start: 0.6961 (mmp-170) cc_final: 0.6651 (mmp-170) REVERT: A 506 MET cc_start: 0.7388 (ttm) cc_final: 0.7100 (ttm) REVERT: A 582 MET cc_start: 0.7098 (mpp) cc_final: 0.6405 (mmm) REVERT: A 619 TRP cc_start: 0.7101 (OUTLIER) cc_final: 0.6619 (t60) REVERT: C 40 TYR cc_start: 0.8482 (t80) cc_final: 0.8171 (t80) REVERT: C 116 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8001 (ttpt) REVERT: C 253 ASP cc_start: 0.7984 (m-30) cc_final: 0.7356 (m-30) REVERT: C 471 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7252 (t80) REVERT: C 577 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7755 (t-90) REVERT: C 659 ILE cc_start: 0.9302 (mt) cc_final: 0.9058 (mt) outliers start: 30 outliers final: 22 residues processed: 139 average time/residue: 0.1678 time to fit residues: 32.0117 Evaluate side-chains 150 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 577 HIS Chi-restraints excluded: chain C residue 617 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.151467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.133785 restraints weight = 12283.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.137569 restraints weight = 6985.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140181 restraints weight = 4636.123| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6983 Z= 0.193 Angle : 0.707 8.327 9467 Z= 0.348 Chirality : 0.045 0.179 1076 Planarity : 0.004 0.042 1200 Dihedral : 4.674 23.896 948 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.66 % Allowed : 21.82 % Favored : 74.53 % 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: -0.71 (0.29), residues: 850 helix: 0.66 (0.29), residues: 349 sheet: -0.46 (0.41), residues: 159 loop : -1.63 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 647 HIS 0.010 0.001 HIS A 545 PHE 0.023 0.002 PHE C 238 TYR 0.030 0.002 TYR A 585 ARG 0.007 0.000 ARG C 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1624.50 seconds wall clock time: 29 minutes 47.51 seconds (1787.51 seconds total)