Starting phenix.real_space_refine on Wed Jan 17 23:23:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qla_14066/01_2024/7qla_14066.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qla_14066/01_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_14066/01_2024/7qla_14066.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qla_14066/01_2024/7qla_14066.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qla_14066/01_2024/7qla_14066.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qla_14066/01_2024/7qla_14066.pdb" } 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 Residue "A ASP 207": "OD1" <-> "OD2" Residue "A TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A ASP 607": "OD1" <-> "OD2" Residue "A TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 465": "OD1" <-> "OD2" Residue "C PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 549": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 4.04, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.82 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: 2.00 Time building geometry restraints manager: 2.70 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: 100.00 - 106.80: 228 106.80 - 113.60: 3875 113.60 - 120.40: 2601 120.40 - 127.20: 2669 127.20 - 134.01: 94 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 2.440 nonbonded pdb=" OG1 THR C 129 " pdb=" O ALA C 132 " model vdw 2.239 2.440 nonbonded pdb=" O ALA C 566 " pdb=" OG SER C 569 " model vdw 2.272 2.440 nonbonded pdb=" OE2 GLU C 651 " pdb=" OG1 THR C 655 " model vdw 2.280 2.440 nonbonded pdb=" OH TYR A 225 " pdb=" OE1 GLN A 302 " model vdw 2.282 2.440 ... (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 ========== 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.610 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 21.640 Find NCS groups from input model: 0.230 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.630 ------------------------------------------------------------------------------- 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 : 0.794 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: 0.1793 time to fit residues: 40.0518 Evaluate side-chains 124 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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: 5.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.0470 overall best weight: 1.1084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1624 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= 0.231 Angle : 0.666 6.941 9467 Z= 0.337 Chirality : 0.045 0.174 1076 Planarity : 0.005 0.039 1200 Dihedral : 4.772 24.385 948 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.03 % Allowed : 11.11 % Favored : 86.86 % 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: -0.98 (0.29), residues: 850 helix: 0.37 (0.28), residues: 343 sheet: -0.71 (0.43), residues: 155 loop : -1.59 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 647 HIS 0.007 0.001 HIS A 545 PHE 0.021 0.002 PHE C 234 TYR 0.025 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 147 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8017 (mpp-170) cc_final: 0.7521 (ptp90) REVERT: A 524 ARG cc_start: 0.8299 (mpp80) cc_final: 0.7371 (mpp80) REVERT: A 559 SER cc_start: 0.9014 (p) cc_final: 0.8788 (p) REVERT: A 587 GLU cc_start: 0.7520 (mp0) cc_final: 0.7164 (mp0) REVERT: A 619 TRP cc_start: 0.6960 (t60) cc_final: 0.6372 (t60) REVERT: C 24 ASN cc_start: 0.8643 (t0) cc_final: 0.8426 (t0) REVERT: C 40 TYR cc_start: 0.8564 (t80) cc_final: 0.8213 (t80) REVERT: C 222 GLN cc_start: 0.7592 (mm110) cc_final: 0.7378 (mm110) REVERT: C 253 ASP cc_start: 0.8036 (m-30) cc_final: 0.7465 (m-30) REVERT: C 349 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7177 (mm-30) REVERT: C 659 ILE cc_start: 0.9352 (mt) cc_final: 0.9123 (mt) outliers start: 15 outliers final: 11 residues processed: 138 average time/residue: 0.1915 time to fit residues: 35.0828 Evaluate side-chains 133 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 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: 0.0770 chunk 24 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 85 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 409 HIS ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6983 Z= 0.173 Angle : 0.629 8.533 9467 Z= 0.309 Chirality : 0.043 0.173 1076 Planarity : 0.004 0.039 1200 Dihedral : 4.606 24.333 948 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.71 % Allowed : 14.63 % 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: -0.78 (0.29), residues: 850 helix: 0.58 (0.29), residues: 337 sheet: -0.41 (0.42), residues: 163 loop : -1.63 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 647 HIS 0.005 0.001 HIS C 99 PHE 0.022 0.002 PHE C 234 TYR 0.021 0.002 TYR A 388 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 154 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.8338 (tpp) cc_final: 0.8005 (tpp) REVERT: A 559 SER cc_start: 0.8975 (p) cc_final: 0.8755 (p) REVERT: A 581 LEU cc_start: 0.7886 (tp) cc_final: 0.7621 (tp) REVERT: A 582 MET cc_start: 0.7133 (mpp) cc_final: 0.6908 (mpp) REVERT: A 587 GLU cc_start: 0.7464 (mp0) cc_final: 0.7168 (mp0) REVERT: A 619 TRP cc_start: 0.7034 (OUTLIER) cc_final: 0.6557 (t60) REVERT: C 40 TYR cc_start: 0.8430 (t80) cc_final: 0.8014 (t80) REVERT: C 95 LYS cc_start: 0.8937 (tppt) cc_final: 0.8649 (tppt) REVERT: C 222 GLN cc_start: 0.7644 (mm110) cc_final: 0.7437 (mm110) REVERT: C 253 ASP cc_start: 0.8006 (m-30) cc_final: 0.7459 (m-30) REVERT: C 659 ILE cc_start: 0.9320 (mt) cc_final: 0.9060 (mt) outliers start: 20 outliers final: 12 residues processed: 140 average time/residue: 0.1851 time to fit residues: 34.7809 Evaluate side-chains 129 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 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 214 SER Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 70 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 370 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2405 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= 0.185 Angle : 0.631 8.848 9467 Z= 0.307 Chirality : 0.043 0.175 1076 Planarity : 0.004 0.041 1200 Dihedral : 4.521 23.858 948 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.39 % Allowed : 15.99 % Favored : 80.62 % 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: 0.62 (0.29), residues: 340 sheet: -0.29 (0.42), residues: 163 loop : -1.66 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 647 HIS 0.004 0.001 HIS C 99 PHE 0.019 0.002 PHE C 541 TYR 0.025 0.001 TYR A 585 ARG 0.007 0.000 ARG A 200 *********************** 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 151 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.8351 (tpp) cc_final: 0.7960 (tpp) REVERT: A 404 ARG cc_start: 0.6821 (mmp-170) cc_final: 0.6440 (mmm160) REVERT: A 559 SER cc_start: 0.9016 (p) cc_final: 0.8779 (p) REVERT: A 581 LEU cc_start: 0.7983 (tp) cc_final: 0.7735 (tp) REVERT: A 582 MET cc_start: 0.7418 (mpp) cc_final: 0.7143 (mpp) REVERT: A 587 GLU cc_start: 0.7469 (mp0) cc_final: 0.7265 (mp0) REVERT: A 619 TRP cc_start: 0.6920 (OUTLIER) cc_final: 0.6455 (t60) REVERT: C 40 TYR cc_start: 0.8438 (t80) cc_final: 0.8057 (t80) REVERT: C 107 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7122 (mm) REVERT: C 253 ASP cc_start: 0.8049 (m-30) cc_final: 0.7496 (m-30) REVERT: C 659 ILE cc_start: 0.9298 (mt) cc_final: 0.9056 (mt) outliers start: 25 outliers final: 15 residues processed: 139 average time/residue: 0.1773 time to fit residues: 33.2870 Evaluate side-chains 134 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 526 THR 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 107 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6983 Z= 0.193 Angle : 0.623 7.707 9467 Z= 0.306 Chirality : 0.043 0.180 1076 Planarity : 0.004 0.040 1200 Dihedral : 4.469 23.603 948 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.07 % Allowed : 17.48 % Favored : 78.46 % 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: -0.64 (0.29), residues: 850 helix: 0.71 (0.29), residues: 340 sheet: -0.24 (0.43), residues: 163 loop : -1.64 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 647 HIS 0.004 0.001 HIS C 99 PHE 0.019 0.002 PHE C 541 TYR 0.024 0.001 TYR A 585 ARG 0.005 0.000 ARG A 200 *********************** 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 155 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.8348 (tpp) cc_final: 0.8110 (tpp) REVERT: A 299 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.7994 (mm) REVERT: A 506 MET cc_start: 0.7348 (ttm) cc_final: 0.6955 (ttm) REVERT: A 559 SER cc_start: 0.9017 (p) cc_final: 0.8787 (p) REVERT: A 582 MET cc_start: 0.7433 (mpp) cc_final: 0.6573 (mmm) REVERT: A 586 GLU cc_start: 0.6363 (pt0) cc_final: 0.6099 (pt0) REVERT: A 587 GLU cc_start: 0.7496 (mp0) cc_final: 0.7248 (mp0) REVERT: A 619 TRP cc_start: 0.6969 (OUTLIER) cc_final: 0.6508 (t60) REVERT: C 40 TYR cc_start: 0.8419 (t80) cc_final: 0.8038 (t80) REVERT: C 253 ASP cc_start: 0.8059 (m-30) cc_final: 0.7477 (m-30) REVERT: C 659 ILE cc_start: 0.9294 (mt) cc_final: 0.9054 (mt) outliers start: 30 outliers final: 16 residues processed: 144 average time/residue: 0.1685 time to fit residues: 33.3423 Evaluate side-chains 142 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 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 628 CYS Chi-restraints excluded: chain C residue 47 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 81 optimal weight: 0.0030 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2775 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= 0.171 Angle : 0.627 8.445 9467 Z= 0.304 Chirality : 0.043 0.190 1076 Planarity : 0.004 0.040 1200 Dihedral : 4.413 23.853 948 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.79 % Allowed : 17.34 % Favored : 78.86 % 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: -0.60 (0.29), residues: 850 helix: 0.78 (0.29), residues: 341 sheet: -0.34 (0.42), residues: 163 loop : -1.61 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 236 HIS 0.004 0.001 HIS C 99 PHE 0.018 0.001 PHE C 541 TYR 0.027 0.001 TYR A 585 ARG 0.004 0.000 ARG A 595 *********************** 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 149 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8340 (tpp) cc_final: 0.8093 (tpp) REVERT: A 299 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.7947 (mm) REVERT: A 404 ARG cc_start: 0.6794 (mmp-170) cc_final: 0.6426 (mmm160) REVERT: A 559 SER cc_start: 0.9008 (p) cc_final: 0.8781 (p) REVERT: A 582 MET cc_start: 0.7396 (mpp) cc_final: 0.6651 (mmm) REVERT: A 619 TRP cc_start: 0.6764 (OUTLIER) cc_final: 0.6359 (t60) REVERT: C 40 TYR cc_start: 0.8366 (t80) cc_final: 0.7937 (t80) REVERT: C 111 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6578 (mpp) REVERT: C 253 ASP cc_start: 0.8065 (m-30) cc_final: 0.7501 (m-30) REVERT: C 659 ILE cc_start: 0.9284 (mt) cc_final: 0.9042 (mt) outliers start: 28 outliers final: 15 residues processed: 135 average time/residue: 0.1718 time to fit residues: 31.7650 Evaluate side-chains 135 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 245 VAL 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 526 THR Chi-restraints excluded: chain A residue 557 CYS 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 111 MET Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 219 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 559 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6983 Z= 0.189 Angle : 0.623 7.167 9467 Z= 0.305 Chirality : 0.044 0.227 1076 Planarity : 0.004 0.044 1200 Dihedral : 4.382 23.418 948 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.25 % Allowed : 18.43 % Favored : 78.32 % 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: -0.51 (0.29), residues: 850 helix: 0.87 (0.29), residues: 341 sheet: -0.26 (0.42), residues: 161 loop : -1.59 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 434 HIS 0.004 0.001 HIS C 99 PHE 0.019 0.002 PHE C 541 TYR 0.028 0.001 TYR A 585 ARG 0.004 0.000 ARG C 289 *********************** 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 148 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.8347 (tpp) cc_final: 0.7959 (tpp) REVERT: A 299 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.7954 (mm) REVERT: A 404 ARG cc_start: 0.6818 (mmp-170) cc_final: 0.6435 (mmm160) REVERT: A 506 MET cc_start: 0.7288 (ttm) cc_final: 0.7075 (ttm) REVERT: A 559 SER cc_start: 0.9020 (p) cc_final: 0.8795 (p) REVERT: A 582 MET cc_start: 0.7349 (mpp) cc_final: 0.6658 (mmm) REVERT: A 619 TRP cc_start: 0.6853 (OUTLIER) cc_final: 0.6425 (t60) REVERT: C 111 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6588 (mpp) REVERT: C 253 ASP cc_start: 0.8093 (m-30) cc_final: 0.7520 (m-30) REVERT: C 659 ILE cc_start: 0.9296 (mt) cc_final: 0.9057 (mt) outliers start: 24 outliers final: 16 residues processed: 134 average time/residue: 0.1743 time to fit residues: 31.9634 Evaluate side-chains 138 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 245 VAL 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 526 THR Chi-restraints excluded: chain A residue 557 CYS 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 47 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 219 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 559 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 80 optimal weight: 0.0970 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6983 Z= 0.178 Angle : 0.644 7.838 9467 Z= 0.312 Chirality : 0.044 0.312 1076 Planarity : 0.004 0.044 1200 Dihedral : 4.368 23.927 948 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.39 % Allowed : 18.97 % Favored : 77.64 % 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: -0.53 (0.29), residues: 850 helix: 0.85 (0.29), residues: 340 sheet: -0.25 (0.42), residues: 164 loop : -1.60 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 434 HIS 0.004 0.001 HIS C 99 PHE 0.022 0.002 PHE C 238 TYR 0.029 0.002 TYR A 585 ARG 0.005 0.000 ARG A 595 *********************** 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 147 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 200 ARG cc_start: 0.7872 (mpp-170) cc_final: 0.7558 (ptp90) REVERT: A 219 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8422 (tptt) REVERT: A 249 MET cc_start: 0.8334 (tpp) cc_final: 0.7957 (tpp) REVERT: A 299 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.7891 (mm) REVERT: A 362 GLU cc_start: 0.8134 (tt0) cc_final: 0.7874 (tt0) REVERT: A 404 ARG cc_start: 0.6773 (mmp-170) cc_final: 0.6514 (mmp-170) REVERT: A 506 MET cc_start: 0.7388 (ttm) cc_final: 0.7078 (ttm) REVERT: A 559 SER cc_start: 0.9009 (p) cc_final: 0.8784 (p) REVERT: A 581 LEU cc_start: 0.8122 (tp) cc_final: 0.7723 (tp) REVERT: A 582 MET cc_start: 0.7271 (mpp) cc_final: 0.6646 (mmm) REVERT: A 619 TRP cc_start: 0.6817 (OUTLIER) cc_final: 0.6428 (t60) REVERT: A 647 VAL cc_start: 0.7902 (t) cc_final: 0.7669 (p) REVERT: C 40 TYR cc_start: 0.8179 (t80) cc_final: 0.7842 (t80) REVERT: C 253 ASP cc_start: 0.8038 (m-30) cc_final: 0.7464 (m-30) REVERT: C 659 ILE cc_start: 0.9293 (mt) cc_final: 0.9050 (mt) outliers start: 25 outliers final: 19 residues processed: 132 average time/residue: 0.2008 time to fit residues: 35.8905 Evaluate side-chains 140 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 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 526 THR Chi-restraints excluded: chain A residue 557 CYS 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 219 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6983 Z= 0.222 Angle : 0.654 8.753 9467 Z= 0.319 Chirality : 0.044 0.257 1076 Planarity : 0.004 0.043 1200 Dihedral : 4.390 23.400 948 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.66 % Allowed : 18.43 % Favored : 77.91 % 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: -0.50 (0.29), residues: 850 helix: 0.90 (0.29), residues: 334 sheet: -0.22 (0.42), residues: 164 loop : -1.59 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 619 HIS 0.008 0.001 HIS A 545 PHE 0.020 0.002 PHE C 541 TYR 0.036 0.002 TYR A 585 ARG 0.005 0.000 ARG A 595 *********************** 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 147 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 219 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8637 (tptt) REVERT: A 249 MET cc_start: 0.8307 (tpp) cc_final: 0.8082 (tpp) REVERT: A 299 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.7943 (mm) REVERT: A 404 ARG cc_start: 0.6843 (mmp-170) cc_final: 0.6617 (mmp-170) REVERT: A 506 MET cc_start: 0.7441 (ttm) cc_final: 0.7107 (ttm) REVERT: A 545 HIS cc_start: 0.7289 (m-70) cc_final: 0.6949 (m170) REVERT: A 559 SER cc_start: 0.9079 (p) cc_final: 0.8834 (p) REVERT: A 582 MET cc_start: 0.7239 (mpp) cc_final: 0.6639 (mmm) REVERT: A 619 TRP cc_start: 0.6892 (OUTLIER) cc_final: 0.6488 (t60) REVERT: C 40 TYR cc_start: 0.8247 (t80) cc_final: 0.7968 (t80) REVERT: C 253 ASP cc_start: 0.8029 (m-30) cc_final: 0.7457 (m-30) REVERT: C 659 ILE cc_start: 0.9304 (mt) cc_final: 0.9058 (mt) outliers start: 27 outliers final: 22 residues processed: 132 average time/residue: 0.2265 time to fit residues: 40.1159 Evaluate side-chains 145 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 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 455 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 THR 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 120 ASP Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 219 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 559 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: 0.8980 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6983 Z= 0.179 Angle : 0.647 9.232 9467 Z= 0.315 Chirality : 0.043 0.251 1076 Planarity : 0.004 0.043 1200 Dihedral : 4.346 23.871 948 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.98 % Allowed : 19.11 % Favored : 77.91 % 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 (0.29), residues: 850 helix: 0.90 (0.29), residues: 334 sheet: -0.18 (0.42), residues: 165 loop : -1.58 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 236 HIS 0.005 0.001 HIS A 545 PHE 0.017 0.002 PHE C 541 TYR 0.034 0.002 TYR A 585 ARG 0.006 0.000 ARG A 238 ********************** 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 141 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 219 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8444 (tptt) REVERT: A 249 MET cc_start: 0.8313 (tpp) cc_final: 0.8079 (tpp) REVERT: A 299 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7834 (mm) REVERT: A 308 MET cc_start: 0.8318 (tpp) cc_final: 0.8073 (tpp) REVERT: A 404 ARG cc_start: 0.6765 (mmp-170) cc_final: 0.6525 (mmp-170) REVERT: A 506 MET cc_start: 0.7425 (ttm) cc_final: 0.7132 (ttm) REVERT: A 545 HIS cc_start: 0.7274 (m-70) cc_final: 0.6891 (m170) REVERT: A 559 SER cc_start: 0.9048 (p) cc_final: 0.8825 (p) REVERT: A 573 GLU cc_start: 0.7919 (pm20) cc_final: 0.6570 (pt0) REVERT: A 582 MET cc_start: 0.7334 (mpp) cc_final: 0.6415 (mmm) REVERT: A 619 TRP cc_start: 0.6849 (OUTLIER) cc_final: 0.6475 (t60) REVERT: A 647 VAL cc_start: 0.7957 (t) cc_final: 0.7729 (p) REVERT: C 40 TYR cc_start: 0.8171 (t80) cc_final: 0.7849 (t80) REVERT: C 253 ASP cc_start: 0.8010 (m-30) cc_final: 0.7457 (m-30) REVERT: C 659 ILE cc_start: 0.9295 (mt) cc_final: 0.9049 (mt) outliers start: 22 outliers final: 18 residues processed: 128 average time/residue: 0.2023 time to fit residues: 35.2243 Evaluate side-chains 138 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 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 526 THR Chi-restraints excluded: chain A residue 557 CYS 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 214 SER Chi-restraints excluded: chain C residue 219 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 559 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: 4.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 60 optimal weight: 0.0030 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 0.0870 overall best weight: 0.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** 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 = 0.3963 r_free = 0.3963 target = 0.154732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.135676 restraints weight = 12139.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.139824 restraints weight = 6971.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.142732 restraints weight = 4615.950| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6983 Z= 0.170 Angle : 0.651 9.116 9467 Z= 0.317 Chirality : 0.043 0.244 1076 Planarity : 0.004 0.044 1200 Dihedral : 4.275 23.993 948 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.25 % Allowed : 19.11 % Favored : 77.64 % 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: -0.41 (0.30), residues: 850 helix: 0.97 (0.29), residues: 336 sheet: -0.14 (0.42), residues: 171 loop : -1.59 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 236 HIS 0.004 0.000 HIS C 99 PHE 0.017 0.002 PHE C 541 TYR 0.033 0.002 TYR A 585 ARG 0.011 0.000 ARG A 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1643.20 seconds wall clock time: 31 minutes 3.87 seconds (1863.87 seconds total)