Starting phenix.real_space_refine on Thu Jun 5 22:27:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qla_14066/06_2025/7qla_14066.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qla_14066/06_2025/7qla_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/cci-nas-00/data/ceres_data/7qla_14066/06_2025/7qla_14066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qla_14066/06_2025/7qla_14066.map" model { file = "/net/cci-nas-00/data/ceres_data/7qla_14066/06_2025/7qla_14066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qla_14066/06_2025/7qla_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-5710/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: 4.43, per 1000 atoms: 0.65 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: 1.82 Conformation dependent library (CDL) restraints added in 1.7 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: 0.76 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: 1.88 Time building geometry restraints manager: 2.05 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: 0.480 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: 20.410 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.350 ------------------------------------------------------------------------------- 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= 0.130 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 Details of bonding type rmsd hydrogen bonds : bond 0.28649 ( 289) hydrogen bonds : angle 9.56075 ( 849) covalent geometry : bond 0.00294 ( 6983) covalent geometry : angle 0.61568 ( 9467) *********************** 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 to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.779 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: 0.1787 time to fit residues: 39.8949 Evaluate side-chains 124 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.152372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.134552 restraints weight = 12385.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.138322 restraints weight = 7107.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.140874 restraints weight = 4731.392| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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= 0.172 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 Details of bonding type rmsd hydrogen bonds : bond 0.05483 ( 289) hydrogen bonds : angle 6.10969 ( 849) covalent geometry : bond 0.00389 ( 6983) covalent geometry : angle 0.68838 ( 9467) *********************** 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 to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 LEU cc_start: 0.8737 (tt) cc_final: 0.8478 (tt) REVERT: A 404 ARG cc_start: 0.6801 (mmp-170) cc_final: 0.6514 (mmp-170) REVERT: A 524 ARG cc_start: 0.8305 (mpp80) cc_final: 0.7427 (mpt-90) REVERT: A 559 SER cc_start: 0.8962 (p) cc_final: 0.8732 (p) REVERT: A 586 GLU cc_start: 0.6567 (pt0) cc_final: 0.6287 (pt0) REVERT: A 587 GLU cc_start: 0.7418 (mp0) cc_final: 0.6947 (mp0) REVERT: A 619 TRP cc_start: 0.6880 (t60) cc_final: 0.6345 (t60) REVERT: C 40 TYR cc_start: 0.8534 (t80) cc_final: 0.8182 (t80) REVERT: C 253 ASP cc_start: 0.8021 (m-30) cc_final: 0.7503 (m-30) outliers start: 15 outliers final: 12 residues processed: 146 average time/residue: 0.1821 time to fit residues: 35.4483 Evaluate side-chains 136 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 41 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 26 optimal weight: 0.0070 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 overall best weight: 0.3598 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.154280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136806 restraints weight = 12489.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140697 restraints weight = 7000.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.143313 restraints weight = 4569.250| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2205 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= 0.121 Angle : 0.635 8.864 9467 Z= 0.316 Chirality : 0.044 0.176 1076 Planarity : 0.004 0.043 1200 Dihedral : 4.726 24.410 948 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.57 % Allowed : 14.63 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.29), residues: 850 helix: 0.36 (0.28), residues: 347 sheet: -0.39 (0.43), residues: 152 loop : -1.65 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 647 HIS 0.007 0.001 HIS A 545 PHE 0.023 0.002 PHE C 234 TYR 0.024 0.002 TYR A 585 ARG 0.006 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 289) hydrogen bonds : angle 5.44116 ( 849) covalent geometry : bond 0.00263 ( 6983) covalent geometry : angle 0.63531 ( 9467) *********************** 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 149 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.840 Fit side-chains REVERT: A 227 ILE cc_start: 0.8075 (mm) cc_final: 0.7818 (mt) REVERT: A 404 ARG cc_start: 0.6663 (mmp-170) cc_final: 0.6329 (mmp-170) REVERT: A 559 SER cc_start: 0.8967 (p) cc_final: 0.8723 (p) REVERT: A 582 MET cc_start: 0.7069 (mpp) cc_final: 0.6816 (mpp) REVERT: A 619 TRP cc_start: 0.7091 (OUTLIER) cc_final: 0.6876 (t60) REVERT: C 40 TYR cc_start: 0.8382 (t80) cc_final: 0.7971 (t80) REVERT: C 95 LYS cc_start: 0.8907 (tppt) cc_final: 0.8705 (tppt) REVERT: C 253 ASP cc_start: 0.7987 (m-30) cc_final: 0.7456 (m-30) outliers start: 19 outliers final: 13 residues processed: 137 average time/residue: 0.1840 time to fit residues: 33.9778 Evaluate side-chains 133 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 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 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 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 76 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.148775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130840 restraints weight = 12628.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.134710 restraints weight = 7108.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.137357 restraints weight = 4680.203| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6983 Z= 0.183 Angle : 0.674 8.954 9467 Z= 0.338 Chirality : 0.045 0.163 1076 Planarity : 0.004 0.045 1200 Dihedral : 4.819 25.166 948 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.20 % Allowed : 15.99 % Favored : 79.81 % 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: -0.89 (0.29), residues: 850 helix: 0.42 (0.28), residues: 348 sheet: -0.60 (0.41), residues: 164 loop : -1.60 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 647 HIS 0.009 0.001 HIS A 545 PHE 0.023 0.002 PHE C 541 TYR 0.033 0.002 TYR A 585 ARG 0.007 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 289) hydrogen bonds : angle 5.35668 ( 849) covalent geometry : bond 0.00420 ( 6983) covalent geometry : angle 0.67371 ( 9467) *********************** 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 159 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ILE cc_start: 0.8109 (mm) cc_final: 0.7836 (mt) REVERT: A 299 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8258 (mm) REVERT: A 404 ARG cc_start: 0.6884 (mmp-170) cc_final: 0.6559 (mmp-170) REVERT: A 582 MET cc_start: 0.7052 (mpp) cc_final: 0.6740 (mpp) REVERT: A 587 GLU cc_start: 0.7472 (mp0) cc_final: 0.7179 (mp0) REVERT: A 619 TRP cc_start: 0.7171 (OUTLIER) cc_final: 0.6767 (t60) REVERT: C 40 TYR cc_start: 0.8548 (t80) cc_final: 0.8220 (t80) REVERT: C 253 ASP cc_start: 0.8058 (m-30) cc_final: 0.7519 (m-30) outliers start: 31 outliers final: 20 residues processed: 144 average time/residue: 0.1845 time to fit residues: 36.2426 Evaluate side-chains 145 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 267 LEU 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 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 57 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 40 optimal weight: 0.0670 chunk 65 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 84 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 73 optimal weight: 0.0010 chunk 75 optimal weight: 0.9990 overall best weight: 0.5528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.152811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.134923 restraints weight = 12415.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.138671 restraints weight = 7054.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141259 restraints weight = 4706.445| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2737 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= 0.121 Angle : 0.663 8.556 9467 Z= 0.326 Chirality : 0.044 0.190 1076 Planarity : 0.004 0.044 1200 Dihedral : 4.660 24.123 948 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.66 % Allowed : 18.29 % Favored : 78.05 % 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: -0.76 (0.29), residues: 850 helix: 0.51 (0.28), residues: 353 sheet: -0.49 (0.41), residues: 165 loop : -1.57 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 647 HIS 0.004 0.001 HIS A 545 PHE 0.019 0.002 PHE A 258 TYR 0.027 0.002 TYR A 585 ARG 0.009 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 289) hydrogen bonds : angle 5.08838 ( 849) covalent geometry : bond 0.00275 ( 6983) covalent geometry : angle 0.66276 ( 9467) *********************** 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 159 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.8147 (tpp) cc_final: 0.7895 (tpp) REVERT: A 404 ARG cc_start: 0.6689 (mmp-170) cc_final: 0.6428 (mmp-170) REVERT: A 506 MET cc_start: 0.7156 (ttm) cc_final: 0.6792 (ttm) REVERT: A 582 MET cc_start: 0.7178 (mpp) cc_final: 0.6270 (mmm) REVERT: A 586 GLU cc_start: 0.5852 (pt0) cc_final: 0.5432 (pt0) REVERT: A 619 TRP cc_start: 0.6902 (OUTLIER) cc_final: 0.6524 (t60) REVERT: C 40 TYR cc_start: 0.8370 (t80) cc_final: 0.7988 (t80) REVERT: C 111 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6581 (mpp) REVERT: C 253 ASP cc_start: 0.7948 (m-30) cc_final: 0.7399 (m-30) outliers start: 27 outliers final: 16 residues processed: 145 average time/residue: 0.1735 time to fit residues: 34.3377 Evaluate side-chains 136 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 387 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 213 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 42 optimal weight: 0.0980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.149240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131360 restraints weight = 12479.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.135184 restraints weight = 7003.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137785 restraints weight = 4602.478| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2913 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= 0.157 Angle : 0.666 7.648 9467 Z= 0.333 Chirality : 0.044 0.174 1076 Planarity : 0.004 0.045 1200 Dihedral : 4.654 24.467 948 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.93 % Allowed : 18.29 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.29), residues: 850 helix: 0.58 (0.28), residues: 354 sheet: -0.51 (0.41), residues: 164 loop : -1.56 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 647 HIS 0.003 0.001 HIS C 99 PHE 0.022 0.002 PHE C 541 TYR 0.031 0.002 TYR A 585 ARG 0.008 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 289) hydrogen bonds : angle 5.09792 ( 849) covalent geometry : bond 0.00362 ( 6983) covalent geometry : angle 0.66623 ( 9467) *********************** 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 156 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.8161 (tpp) cc_final: 0.7930 (tpp) REVERT: A 299 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8232 (mm) REVERT: A 404 ARG cc_start: 0.6807 (mmp-170) cc_final: 0.6514 (mmp-170) REVERT: A 582 MET cc_start: 0.7154 (mpp) cc_final: 0.6284 (mmm) REVERT: A 586 GLU cc_start: 0.5949 (pt0) cc_final: 0.5620 (pt0) REVERT: A 619 TRP cc_start: 0.6942 (OUTLIER) cc_final: 0.6573 (t60) REVERT: C 40 TYR cc_start: 0.8463 (t80) cc_final: 0.8061 (t80) REVERT: C 253 ASP cc_start: 0.7977 (m-30) cc_final: 0.7422 (m-30) REVERT: C 349 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6844 (mm-30) outliers start: 29 outliers final: 20 residues processed: 142 average time/residue: 0.1745 time to fit residues: 33.8416 Evaluate side-chains 144 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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 47 LEU Chi-restraints excluded: chain C residue 195 LEU 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 555 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 4 optimal weight: 0.0270 chunk 26 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.151521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.133662 restraints weight = 12255.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137494 restraints weight = 6923.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140111 restraints weight = 4562.783| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3045 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= 0.127 Angle : 0.662 7.352 9467 Z= 0.328 Chirality : 0.044 0.184 1076 Planarity : 0.004 0.042 1200 Dihedral : 4.579 23.614 948 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.93 % Allowed : 18.83 % Favored : 77.24 % 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: 0.56 (0.28), residues: 347 sheet: -0.64 (0.40), residues: 165 loop : -1.58 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 647 HIS 0.004 0.001 HIS A 545 PHE 0.018 0.002 PHE C 541 TYR 0.027 0.002 TYR A 585 ARG 0.009 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 289) hydrogen bonds : angle 4.97309 ( 849) covalent geometry : bond 0.00295 ( 6983) covalent geometry : angle 0.66213 ( 9467) *********************** 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 164 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.709 Fit side-chains REVERT: A 219 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8550 (tptt) REVERT: A 249 MET cc_start: 0.8086 (tpp) cc_final: 0.7858 (tpp) REVERT: A 299 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8087 (mm) REVERT: A 404 ARG cc_start: 0.6667 (mmp-170) cc_final: 0.6409 (mmp-170) REVERT: A 506 MET cc_start: 0.7075 (ttm) cc_final: 0.6829 (ttm) REVERT: A 582 MET cc_start: 0.7443 (mpp) cc_final: 0.6370 (mmm) REVERT: A 586 GLU cc_start: 0.5871 (pt0) cc_final: 0.5560 (pt0) REVERT: A 619 TRP cc_start: 0.6860 (OUTLIER) cc_final: 0.6539 (t60) REVERT: C 40 TYR cc_start: 0.8349 (t80) cc_final: 0.7978 (t80) REVERT: C 253 ASP cc_start: 0.7898 (m-30) cc_final: 0.7338 (m-30) outliers start: 29 outliers final: 20 residues processed: 150 average time/residue: 0.1840 time to fit residues: 37.2746 Evaluate side-chains 142 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 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 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 C residue 195 LEU 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 555 SER Chi-restraints excluded: chain C residue 559 THR 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 3 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN A 376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.148516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.130266 restraints weight = 12576.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.134113 restraints weight = 7132.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.136722 restraints weight = 4710.055| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6983 Z= 0.177 Angle : 0.712 7.547 9467 Z= 0.356 Chirality : 0.046 0.254 1076 Planarity : 0.004 0.045 1200 Dihedral : 4.704 24.773 948 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.61 % Allowed : 18.56 % Favored : 76.83 % 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: 0.60 (0.28), residues: 350 sheet: -0.67 (0.40), residues: 164 loop : -1.57 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 647 HIS 0.009 0.001 HIS A 545 PHE 0.022 0.002 PHE C 541 TYR 0.034 0.002 TYR A 585 ARG 0.012 0.001 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 289) hydrogen bonds : angle 5.02504 ( 849) covalent geometry : bond 0.00416 ( 6983) covalent geometry : angle 0.71156 ( 9467) *********************** 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 to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 219 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8566 (tptt) REVERT: A 249 MET cc_start: 0.8108 (tpp) cc_final: 0.7888 (tpp) REVERT: A 299 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8138 (mm) REVERT: A 404 ARG cc_start: 0.6794 (mmp-170) cc_final: 0.6502 (mmp-170) REVERT: A 506 MET cc_start: 0.7244 (ttm) cc_final: 0.6892 (ttm) REVERT: A 582 MET cc_start: 0.7122 (mpp) cc_final: 0.6246 (mmm) REVERT: A 586 GLU cc_start: 0.5915 (pt0) cc_final: 0.5683 (pt0) REVERT: A 619 TRP cc_start: 0.7155 (OUTLIER) cc_final: 0.6767 (t60) REVERT: C 40 TYR cc_start: 0.8447 (t80) cc_final: 0.8117 (t80) REVERT: C 253 ASP cc_start: 0.7919 (m-30) cc_final: 0.7368 (m-30) REVERT: C 471 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7442 (t80) outliers start: 34 outliers final: 24 residues processed: 145 average time/residue: 0.1743 time to fit residues: 34.2914 Evaluate side-chains 152 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 587 GLU 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 219 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 559 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 14 optimal weight: 4.9990 chunk 54 optimal weight: 0.0050 chunk 1 optimal weight: 5.9990 chunk 56 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.153990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136825 restraints weight = 12516.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.140544 restraints weight = 7141.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.143082 restraints weight = 4723.850| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3283 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= 0.125 Angle : 0.707 9.984 9467 Z= 0.346 Chirality : 0.044 0.242 1076 Planarity : 0.004 0.041 1200 Dihedral : 4.573 24.174 948 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.07 % Allowed : 19.65 % 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: -0.63 (0.29), residues: 850 helix: 0.67 (0.29), residues: 347 sheet: -0.45 (0.41), residues: 159 loop : -1.49 (0.34), residues: 344 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 0.017 0.002 PHE C 234 TYR 0.032 0.002 TYR A 585 ARG 0.013 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 289) hydrogen bonds : angle 4.90946 ( 849) covalent geometry : bond 0.00289 ( 6983) covalent geometry : angle 0.70705 ( 9467) *********************** 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 to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.8013 (tpp) cc_final: 0.7689 (tpp) REVERT: A 299 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8033 (mm) REVERT: A 404 ARG cc_start: 0.6554 (mmp-170) cc_final: 0.6310 (mmp-170) REVERT: A 506 MET cc_start: 0.7114 (ttm) cc_final: 0.6814 (ttm) REVERT: A 582 MET cc_start: 0.7405 (mpp) cc_final: 0.6425 (mmm) REVERT: A 586 GLU cc_start: 0.5778 (pt0) cc_final: 0.5505 (pt0) REVERT: A 619 TRP cc_start: 0.6907 (OUTLIER) cc_final: 0.6600 (t60) REVERT: C 40 TYR cc_start: 0.8229 (t80) cc_final: 0.7801 (t80) REVERT: C 47 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6483 (tt) REVERT: C 236 ASP cc_start: 0.7667 (t70) cc_final: 0.7373 (t0) REVERT: C 253 ASP cc_start: 0.7882 (m-30) cc_final: 0.7418 (m-30) REVERT: C 471 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.6688 (t80) outliers start: 30 outliers final: 20 residues processed: 145 average time/residue: 0.1691 time to fit residues: 33.3383 Evaluate side-chains 145 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 387 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 214 SER 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 471 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 569 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.0470 chunk 26 optimal weight: 0.7980 chunk 53 optimal weight: 0.0470 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.151365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.133782 restraints weight = 12442.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.137580 restraints weight = 7006.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140194 restraints weight = 4603.290| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3340 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= 0.141 Angle : 0.704 9.379 9467 Z= 0.347 Chirality : 0.045 0.258 1076 Planarity : 0.004 0.043 1200 Dihedral : 4.572 23.325 948 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.07 % Allowed : 19.92 % Favored : 76.02 % 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: -0.67 (0.29), residues: 850 helix: 0.61 (0.28), residues: 349 sheet: -0.42 (0.41), residues: 159 loop : -1.52 (0.34), 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 0.026 0.002 PHE C 238 TYR 0.031 0.002 TYR A 585 ARG 0.007 0.000 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 289) hydrogen bonds : angle 4.90408 ( 849) covalent geometry : bond 0.00330 ( 6983) covalent geometry : angle 0.70392 ( 9467) ********************** 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 to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 299 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8112 (mm) REVERT: A 404 ARG cc_start: 0.6603 (mmp-170) cc_final: 0.6344 (mmp-170) REVERT: A 506 MET cc_start: 0.7181 (ttm) cc_final: 0.6855 (ttm) REVERT: A 582 MET cc_start: 0.7433 (mpp) cc_final: 0.6650 (mmm) REVERT: A 619 TRP cc_start: 0.6954 (OUTLIER) cc_final: 0.6572 (t60) REVERT: C 40 TYR cc_start: 0.8371 (t80) cc_final: 0.8021 (t80) REVERT: C 253 ASP cc_start: 0.7905 (m-30) cc_final: 0.7337 (m-30) REVERT: C 471 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.6986 (t80) REVERT: C 577 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.7533 (t-90) outliers start: 30 outliers final: 23 residues processed: 138 average time/residue: 0.1744 time to fit residues: 32.9013 Evaluate side-chains 150 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 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 587 GLU Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain C residue 31 ASP 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 329 VAL 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 559 THR Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 577 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 42 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.150947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132968 restraints weight = 12465.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136845 restraints weight = 7056.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139493 restraints weight = 4641.612| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3409 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= 0.147 Angle : 0.713 9.661 9467 Z= 0.351 Chirality : 0.045 0.258 1076 Planarity : 0.004 0.043 1200 Dihedral : 4.591 23.797 948 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.79 % Allowed : 20.60 % Favored : 75.61 % 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: -0.67 (0.29), residues: 850 helix: 0.63 (0.29), residues: 347 sheet: -0.58 (0.40), residues: 166 loop : -1.46 (0.34), residues: 337 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 0.031 0.002 TYR A 585 ARG 0.009 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 289) hydrogen bonds : angle 4.90992 ( 849) covalent geometry : bond 0.00347 ( 6983) covalent geometry : angle 0.71340 ( 9467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2232.36 seconds wall clock time: 39 minutes 32.64 seconds (2372.64 seconds total)