Starting phenix.real_space_refine on Thu Sep 18 23:16:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j60_61158/09_2025/9j60_61158.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j60_61158/09_2025/9j60_61158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j60_61158/09_2025/9j60_61158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j60_61158/09_2025/9j60_61158.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j60_61158/09_2025/9j60_61158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j60_61158/09_2025/9j60_61158.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.070 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: 5 Type Number sf(0) Gaussians S 75 5.16 5 C 6889 2.51 5 N 1837 2.21 5 O 1991 1.98 5 H 10175 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20967 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 10187 Classifications: {'peptide': 656} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 619} Chain breaks: 3 Chain: "B" Number of atoms: 10780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 10780 Classifications: {'peptide': 698} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 657} Chain breaks: 1 Time building chain proxies: 3.68, per 1000 atoms: 0.18 Number of scatterers: 20967 At special positions: 0 Unit cell: (67.2, 69.72, 194.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 O 1991 8.00 N 1837 7.00 C 6889 6.00 H 10175 1.00 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: 1.75 Conformation dependent library (CDL) restraints added in 548.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 15 sheets defined 32.5% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.082A pdb=" N THR A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 5.865A pdb=" N SER A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 262 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 272 removed outlier: 3.503A pdb=" N ALA A 272 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 274 No H-bonds generated for 'chain 'A' and resid 273 through 274' Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 333 through 349 Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.831A pdb=" N ASN A 380 " --> pdb=" O ARG A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 425 Processing helix chain 'A' and resid 471 through 477 Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.756A pdb=" N ARG A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 523 " --> pdb=" O ARG A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 537 removed outlier: 3.548A pdb=" N CYS A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 564 through 569 removed outlier: 3.765A pdb=" N VAL A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 580 Processing helix chain 'A' and resid 603 through 624 removed outlier: 3.572A pdb=" N SER A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 651 through 655 Processing helix chain 'A' and resid 657 through 662 removed outlier: 3.807A pdb=" N GLU A 662 " --> pdb=" O TRP A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 681 Processing helix chain 'A' and resid 770 through 777 Processing helix chain 'A' and resid 778 through 783 Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.848A pdb=" N GLU B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 245 Processing helix chain 'B' and resid 251 through 257 removed outlier: 4.266A pdb=" N THR B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 268 through 274 removed outlier: 3.686A pdb=" N ILE B 273 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 283 removed outlier: 3.550A pdb=" N LEU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.607A pdb=" N SER B 325 " --> pdb=" O ILE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 333 through 350 Processing helix chain 'B' and resid 374 through 384 removed outlier: 3.731A pdb=" N ILE B 378 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 380 " --> pdb=" O ARG B 376 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N SER B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR B 382 " --> pdb=" O ILE B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 423 removed outlier: 3.560A pdb=" N GLU B 411 " --> pdb=" O PRO B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 477 Processing helix chain 'B' and resid 511 through 524 removed outlier: 3.660A pdb=" N ARG B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 537 removed outlier: 3.590A pdb=" N CYS B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 549 through 551 No H-bonds generated for 'chain 'B' and resid 549 through 551' Processing helix chain 'B' and resid 566 through 570 Processing helix chain 'B' and resid 603 through 624 removed outlier: 3.505A pdb=" N SER B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.613A pdb=" N TYR B 636 " --> pdb=" O GLY B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 655 Processing helix chain 'B' and resid 659 through 664 removed outlier: 3.652A pdb=" N GLU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.551A pdb=" N GLN B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 removed outlier: 3.611A pdb=" N GLY B 685 " --> pdb=" O GLU B 682 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 682 through 685' Processing helix chain 'B' and resid 770 through 777 Processing helix chain 'B' and resid 778 through 783 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.560A pdb=" N PHE A 160 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.560A pdb=" N PHE A 160 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.323A pdb=" N TYR A 248 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY A 428 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU A 509 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER A 553 " --> pdb=" O VAL A 627 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET A 629 " --> pdb=" O SER A 553 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASN A 555 " --> pdb=" O MET A 629 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N TYR A 631 " --> pdb=" O ASN A 555 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 293 through 294 removed outlier: 7.142A pdb=" N SER A 319 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 695 through 698 removed outlier: 3.700A pdb=" N ALA A 715 " --> pdb=" O HIS A 698 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU A 725 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER A 794 " --> pdb=" O ASP A 754 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP A 754 " --> pdb=" O SER A 794 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE A 796 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 737 through 740 Processing sheet with id=AA9, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.602A pdb=" N PHE B 160 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.602A pdb=" N PHE B 160 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.566A pdb=" N ALA B 124 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 178 through 179 Processing sheet with id=AB4, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.312A pdb=" N TYR B 248 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 428 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE B 429 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU B 485 " --> pdb=" O SER B 508 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N TRP B 510 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ALA B 487 " --> pdb=" O TRP B 510 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU B 509 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 630 " --> pdb=" O ILE B 247 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 695 through 698 removed outlier: 3.633A pdb=" N ALA B 715 " --> pdb=" O HIS B 698 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU B 725 " --> pdb=" O LEU B 799 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N SER B 794 " --> pdb=" O ASP B 754 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP B 754 " --> pdb=" O SER B 794 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 796 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 737 through 740 357 hydrogen bonds defined for protein. 927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10139 1.03 - 1.23: 82 1.23 - 1.42: 4968 1.42 - 1.62: 5996 1.62 - 1.81: 114 Bond restraints: 21299 Sorted by residual: bond pdb=" N ARG A 95 " pdb=" CA ARG A 95 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N ARG B 87 " pdb=" CA ARG B 87 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 bond pdb=" N ARG A 95 " pdb=" H ARG A 95 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" N ARG B 87 " pdb=" H ARG B 87 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" CA GLY A 562 " pdb=" C GLY A 562 " ideal model delta sigma weight residual 1.520 1.508 0.012 1.10e-02 8.26e+03 1.11e+00 ... (remaining 21294 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 36580 1.31 - 2.63: 1483 2.63 - 3.94: 132 3.94 - 5.26: 15 5.26 - 6.57: 3 Bond angle restraints: 38213 Sorted by residual: angle pdb=" N ILE B 436 " pdb=" CA ILE B 436 " pdb=" C ILE B 436 " ideal model delta sigma weight residual 113.53 106.96 6.57 9.80e-01 1.04e+00 4.50e+01 angle pdb=" N VAL A 557 " pdb=" CA VAL A 557 " pdb=" C VAL A 557 " ideal model delta sigma weight residual 113.47 109.12 4.35 1.01e+00 9.80e-01 1.85e+01 angle pdb=" N ASP B 767 " pdb=" CA ASP B 767 " pdb=" C ASP B 767 " ideal model delta sigma weight residual 114.56 109.35 5.21 1.27e+00 6.20e-01 1.68e+01 angle pdb=" CA ASP A 720 " pdb=" C ASP A 720 " pdb=" N GLU A 721 " ideal model delta sigma weight residual 115.63 120.60 -4.97 1.36e+00 5.41e-01 1.33e+01 angle pdb=" CA ASP A 720 " pdb=" C ASP A 720 " pdb=" O ASP A 720 " ideal model delta sigma weight residual 121.88 117.91 3.97 1.30e+00 5.92e-01 9.34e+00 ... (remaining 38208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 9382 17.68 - 35.35: 570 35.35 - 53.03: 193 53.03 - 70.71: 55 70.71 - 88.39: 8 Dihedral angle restraints: 10208 sinusoidal: 5316 harmonic: 4892 Sorted by residual: dihedral pdb=" CA LEU B 373 " pdb=" C LEU B 373 " pdb=" N SER B 374 " pdb=" CA SER B 374 " ideal model delta harmonic sigma weight residual -180.00 -154.53 -25.47 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA GLY A 111 " pdb=" C GLY A 111 " pdb=" N GLY A 112 " pdb=" CA GLY A 112 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ASP A 110 " pdb=" C ASP A 110 " pdb=" N GLY A 111 " pdb=" CA GLY A 111 " ideal model delta harmonic sigma weight residual -180.00 -155.92 -24.08 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 10205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 740 0.028 - 0.056: 526 0.056 - 0.084: 160 0.084 - 0.113: 63 0.113 - 0.141: 32 Chirality restraints: 1521 Sorted by residual: chirality pdb=" CA ILE B 554 " pdb=" N ILE B 554 " pdb=" C ILE B 554 " pdb=" CB ILE B 554 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA VAL B 246 " pdb=" N VAL B 246 " pdb=" C VAL B 246 " pdb=" CB VAL B 246 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA VAL A 246 " pdb=" N VAL A 246 " pdb=" C VAL A 246 " pdb=" CB VAL A 246 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 1518 not shown) Planarity restraints: 3259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 343 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C PHE B 343 " 0.027 2.00e-02 2.50e+03 pdb=" O PHE B 343 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 344 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 344 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.15e+00 pdb=" C VAL A 344 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL A 344 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG A 345 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 406 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO B 407 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " -0.020 5.00e-02 4.00e+02 ... (remaining 3256 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 808 2.18 - 2.78: 39995 2.78 - 3.39: 56481 3.39 - 3.99: 78111 3.99 - 4.60: 121514 Nonbonded interactions: 296909 Sorted by model distance: nonbonded pdb=" HZ2 LYS B 574 " pdb=" O ASP B 585 " model vdw 1.569 2.450 nonbonded pdb=" OD2 ASP B 357 " pdb="HH21 ARG B 430 " model vdw 1.575 2.450 nonbonded pdb=" O HIS A 649 " pdb="HD21 ASN A 654 " model vdw 1.605 2.450 nonbonded pdb="HD21 ASN A 576 " pdb=" O ASP A 585 " model vdw 1.631 2.450 nonbonded pdb="HD21 ASN B 405 " pdb=" O ARG B 439 " model vdw 1.638 2.450 ... (remaining 296904 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 95 through 386 or resid 394 through 434 or resid 470 throu \ gh 488 or resid 499 through 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 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: 0.130 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.900 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 0.004 0.034 11124 Z= 0.190 Angle : 0.622 6.572 15089 Z= 0.363 Chirality : 0.043 0.141 1521 Planarity : 0.005 0.044 1987 Dihedral : 13.420 88.387 3982 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.96 % Allowed : 11.12 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.22), residues: 1342 helix: -0.25 (0.29), residues: 313 sheet: -0.14 (0.32), residues: 253 loop : -0.79 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 430 TYR 0.019 0.002 TYR A 170 PHE 0.016 0.002 PHE B 402 TRP 0.011 0.001 TRP B 551 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00428 (11124) covalent geometry : angle 0.62245 (15089) hydrogen bonds : bond 0.18822 ( 355) hydrogen bonds : angle 8.28050 ( 927) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.6620 (mtp) cc_final: 0.5441 (mpp) REVERT: A 349 LYS cc_start: 0.7487 (mtmt) cc_final: 0.6595 (tttm) REVERT: A 413 ILE cc_start: 0.7704 (mt) cc_final: 0.7465 (mm) REVERT: A 418 ARG cc_start: 0.7492 (ttp-110) cc_final: 0.7143 (mtp-110) REVERT: A 622 MET cc_start: 0.8932 (mmm) cc_final: 0.7929 (mmt) REVERT: B 139 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7173 (tm-30) REVERT: B 330 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.7586 (tpt-90) outliers start: 11 outliers final: 8 residues processed: 132 average time/residue: 1.0716 time to fit residues: 154.3155 Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 620 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.0270 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.0370 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.162992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115745 restraints weight = 35667.354| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.26 r_work: 0.3317 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11124 Z= 0.099 Angle : 0.491 6.661 15089 Z= 0.260 Chirality : 0.041 0.148 1521 Planarity : 0.004 0.037 1987 Dihedral : 4.804 34.739 1490 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.96 % Allowed : 10.25 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.23), residues: 1342 helix: 0.66 (0.29), residues: 319 sheet: -0.00 (0.33), residues: 252 loop : -0.50 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 678 TYR 0.010 0.001 TYR B 652 PHE 0.013 0.001 PHE B 130 TRP 0.006 0.001 TRP A 420 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00207 (11124) covalent geometry : angle 0.49134 (15089) hydrogen bonds : bond 0.04263 ( 355) hydrogen bonds : angle 6.20732 ( 927) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.6611 (mtp) cc_final: 0.5408 (mpp) REVERT: A 349 LYS cc_start: 0.7444 (mtmt) cc_final: 0.6744 (tttm) REVERT: A 418 ARG cc_start: 0.7675 (ttp-110) cc_final: 0.7235 (mtp-110) REVERT: A 585 ASP cc_start: 0.6639 (t0) cc_final: 0.6377 (t0) REVERT: A 660 LYS cc_start: 0.7344 (mmtp) cc_final: 0.6924 (mtpt) REVERT: A 798 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: B 139 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7224 (tm-30) REVERT: B 330 ARG cc_start: 0.7939 (ttp-170) cc_final: 0.7625 (ttt90) REVERT: B 513 LYS cc_start: 0.8388 (mttm) cc_final: 0.8124 (mtpt) REVERT: B 721 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7641 (tp30) outliers start: 11 outliers final: 3 residues processed: 139 average time/residue: 1.0334 time to fit residues: 156.1466 Evaluate side-chains 126 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 95 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.158145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110525 restraints weight = 35829.596| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.24 r_work: 0.3229 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11124 Z= 0.215 Angle : 0.563 7.234 15089 Z= 0.299 Chirality : 0.044 0.157 1521 Planarity : 0.005 0.045 1987 Dihedral : 4.842 37.482 1481 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.30 % Allowed : 10.86 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.22), residues: 1342 helix: 0.45 (0.30), residues: 311 sheet: -0.14 (0.32), residues: 250 loop : -0.82 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 430 TYR 0.015 0.002 TYR A 543 PHE 0.020 0.002 PHE B 130 TRP 0.014 0.001 TRP B 551 HIS 0.008 0.002 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00527 (11124) covalent geometry : angle 0.56297 (15089) hydrogen bonds : bond 0.05601 ( 355) hydrogen bonds : angle 6.21443 ( 927) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7366 (tpt) REVERT: A 307 MET cc_start: 0.6765 (mtp) cc_final: 0.5492 (mpp) REVERT: A 349 LYS cc_start: 0.7630 (mtmt) cc_final: 0.6829 (tttm) REVERT: A 418 ARG cc_start: 0.7620 (ttp-110) cc_final: 0.7227 (mtp-110) REVERT: A 585 ASP cc_start: 0.6602 (t0) cc_final: 0.6366 (t0) REVERT: A 587 GLU cc_start: 0.6591 (tp30) cc_final: 0.6390 (pt0) REVERT: A 622 MET cc_start: 0.8913 (mmm) cc_final: 0.8042 (mmt) REVERT: A 660 LYS cc_start: 0.7258 (mmtp) cc_final: 0.6805 (mtpt) REVERT: A 798 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: B 139 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7232 (tm-30) REVERT: B 305 SER cc_start: 0.8692 (t) cc_final: 0.8294 (m) REVERT: B 330 ARG cc_start: 0.8105 (ttp-170) cc_final: 0.7806 (ttt90) outliers start: 15 outliers final: 8 residues processed: 130 average time/residue: 1.0104 time to fit residues: 143.4954 Evaluate side-chains 127 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 374 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 97 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.158634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111203 restraints weight = 36001.695| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.26 r_work: 0.3232 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11124 Z= 0.177 Angle : 0.537 7.423 15089 Z= 0.283 Chirality : 0.043 0.155 1521 Planarity : 0.004 0.041 1987 Dihedral : 4.833 40.681 1481 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 1.48 % Allowed : 10.69 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.22), residues: 1342 helix: 0.39 (0.29), residues: 318 sheet: -0.24 (0.32), residues: 254 loop : -0.89 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 430 TYR 0.014 0.002 TYR B 652 PHE 0.017 0.002 PHE B 130 TRP 0.011 0.001 TRP B 551 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00432 (11124) covalent geometry : angle 0.53716 (15089) hydrogen bonds : bond 0.04962 ( 355) hydrogen bonds : angle 6.14088 ( 927) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7406 (tpt) REVERT: A 307 MET cc_start: 0.6869 (mtp) cc_final: 0.5548 (mpp) REVERT: A 349 LYS cc_start: 0.7681 (mtmt) cc_final: 0.6896 (tttm) REVERT: A 418 ARG cc_start: 0.7650 (ttp-110) cc_final: 0.7258 (mtp-110) REVERT: A 585 ASP cc_start: 0.6643 (t0) cc_final: 0.6348 (t0) REVERT: A 622 MET cc_start: 0.8843 (mmm) cc_final: 0.8094 (mmt) REVERT: A 798 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8176 (mp0) REVERT: B 139 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7224 (tm-30) REVERT: B 305 SER cc_start: 0.8682 (t) cc_final: 0.8273 (m) REVERT: B 330 ARG cc_start: 0.8113 (ttp-170) cc_final: 0.7817 (ttt90) REVERT: B 513 LYS cc_start: 0.8547 (mttm) cc_final: 0.8293 (mtpt) REVERT: B 719 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7967 (mtmm) outliers start: 17 outliers final: 7 residues processed: 130 average time/residue: 1.0229 time to fit residues: 144.9216 Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 719 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.158517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111333 restraints weight = 35815.025| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.22 r_work: 0.3257 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11124 Z= 0.163 Angle : 0.528 7.749 15089 Z= 0.278 Chirality : 0.043 0.155 1521 Planarity : 0.004 0.042 1987 Dihedral : 4.791 45.015 1481 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.65 % Allowed : 10.95 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.22), residues: 1342 helix: 0.39 (0.29), residues: 319 sheet: -0.28 (0.32), residues: 255 loop : -0.91 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 430 TYR 0.015 0.001 TYR B 652 PHE 0.018 0.002 PHE B 130 TRP 0.010 0.001 TRP B 551 HIS 0.010 0.001 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00399 (11124) covalent geometry : angle 0.52768 (15089) hydrogen bonds : bond 0.04803 ( 355) hydrogen bonds : angle 6.05644 ( 927) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7089 (tt0) REVERT: A 168 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7416 (tpt) REVERT: A 307 MET cc_start: 0.6865 (mtp) cc_final: 0.5556 (mpp) REVERT: A 330 ARG cc_start: 0.6935 (ttm-80) cc_final: 0.6635 (mtm-85) REVERT: A 349 LYS cc_start: 0.7702 (mtmt) cc_final: 0.6916 (tttm) REVERT: A 359 VAL cc_start: 0.8122 (t) cc_final: 0.7655 (p) REVERT: A 418 ARG cc_start: 0.7728 (ttp-110) cc_final: 0.7338 (mtp-110) REVERT: A 585 ASP cc_start: 0.6534 (t0) cc_final: 0.6242 (t0) REVERT: A 622 MET cc_start: 0.8826 (mmm) cc_final: 0.8091 (mmt) REVERT: A 660 LYS cc_start: 0.7386 (mtpt) cc_final: 0.6865 (mtpt) REVERT: A 798 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: B 126 SER cc_start: 0.8946 (p) cc_final: 0.8735 (t) REVERT: B 139 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7223 (tm-30) REVERT: B 305 SER cc_start: 0.8711 (t) cc_final: 0.8307 (m) REVERT: B 330 ARG cc_start: 0.8121 (ttp-170) cc_final: 0.7868 (ttt90) REVERT: B 513 LYS cc_start: 0.8523 (mttm) cc_final: 0.8281 (mtpt) REVERT: B 719 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7982 (mtmm) outliers start: 19 outliers final: 8 residues processed: 134 average time/residue: 1.0141 time to fit residues: 148.1180 Evaluate side-chains 132 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 719 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 124 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 425 HIS B 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.157100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109805 restraints weight = 36108.888| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.24 r_work: 0.3237 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11124 Z= 0.207 Angle : 0.557 7.859 15089 Z= 0.295 Chirality : 0.044 0.156 1521 Planarity : 0.005 0.043 1987 Dihedral : 4.934 49.170 1481 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.56 % Allowed : 11.03 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.22), residues: 1342 helix: 0.27 (0.29), residues: 320 sheet: -0.31 (0.32), residues: 255 loop : -1.05 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 612 TYR 0.014 0.002 TYR A 543 PHE 0.018 0.002 PHE B 130 TRP 0.012 0.001 TRP B 551 HIS 0.007 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00509 (11124) covalent geometry : angle 0.55708 (15089) hydrogen bonds : bond 0.05288 ( 355) hydrogen bonds : angle 6.12522 ( 927) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: A 168 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7443 (tpt) REVERT: A 307 MET cc_start: 0.6933 (mtp) cc_final: 0.5630 (mpp) REVERT: A 330 ARG cc_start: 0.7026 (ttm-80) cc_final: 0.6616 (mtm-85) REVERT: A 349 LYS cc_start: 0.7675 (mtmt) cc_final: 0.6853 (tttm) REVERT: A 359 VAL cc_start: 0.8138 (t) cc_final: 0.7677 (p) REVERT: A 418 ARG cc_start: 0.7724 (ttp-110) cc_final: 0.7341 (mtp-110) REVERT: A 585 ASP cc_start: 0.6607 (t0) cc_final: 0.6328 (t0) REVERT: A 622 MET cc_start: 0.8812 (mmm) cc_final: 0.8221 (mmt) REVERT: A 798 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: B 100 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7901 (mmm) REVERT: B 139 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7249 (tm-30) REVERT: B 305 SER cc_start: 0.8760 (t) cc_final: 0.8350 (m) REVERT: B 330 ARG cc_start: 0.8144 (ttp-170) cc_final: 0.7882 (ttt90) REVERT: B 379 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7118 (m-30) REVERT: B 513 LYS cc_start: 0.8560 (mttm) cc_final: 0.8303 (mtpt) REVERT: B 719 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.7965 (mtmm) outliers start: 18 outliers final: 7 residues processed: 130 average time/residue: 1.0194 time to fit residues: 144.4482 Evaluate side-chains 131 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 719 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN B 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.157004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109698 restraints weight = 36054.542| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.24 r_work: 0.3218 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11124 Z= 0.209 Angle : 0.563 7.524 15089 Z= 0.297 Chirality : 0.044 0.157 1521 Planarity : 0.005 0.044 1987 Dihedral : 4.997 53.349 1481 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.74 % Favored : 94.19 % Rotamer: Outliers : 1.56 % Allowed : 11.12 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.22), residues: 1342 helix: 0.27 (0.29), residues: 320 sheet: -0.37 (0.32), residues: 255 loop : -1.12 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 430 TYR 0.018 0.002 TYR B 652 PHE 0.018 0.002 PHE B 130 TRP 0.012 0.001 TRP B 551 HIS 0.007 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00514 (11124) covalent geometry : angle 0.56291 (15089) hydrogen bonds : bond 0.05299 ( 355) hydrogen bonds : angle 6.10478 ( 927) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7367 (tt0) cc_final: 0.7082 (tt0) REVERT: A 168 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7363 (tpt) REVERT: A 307 MET cc_start: 0.6993 (mtp) cc_final: 0.5708 (mpp) REVERT: A 330 ARG cc_start: 0.7104 (ttm-80) cc_final: 0.6726 (mtm-85) REVERT: A 349 LYS cc_start: 0.7723 (mtmt) cc_final: 0.6876 (tttm) REVERT: A 359 VAL cc_start: 0.8222 (t) cc_final: 0.7771 (p) REVERT: A 418 ARG cc_start: 0.7722 (ttp-110) cc_final: 0.7342 (mtp-110) REVERT: A 585 ASP cc_start: 0.6581 (t0) cc_final: 0.6322 (t0) REVERT: A 622 MET cc_start: 0.8801 (mmm) cc_final: 0.8189 (mmt) REVERT: A 798 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: B 139 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7251 (tm-30) REVERT: B 305 SER cc_start: 0.8752 (t) cc_final: 0.8348 (m) REVERT: B 330 ARG cc_start: 0.8135 (ttp-170) cc_final: 0.7887 (ttt90) REVERT: B 379 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7138 (m-30) REVERT: B 513 LYS cc_start: 0.8562 (mttm) cc_final: 0.8310 (mtpt) REVERT: B 719 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.7977 (mtmm) outliers start: 18 outliers final: 10 residues processed: 132 average time/residue: 0.9780 time to fit residues: 140.4703 Evaluate side-chains 132 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 719 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 127 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 82 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN B 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.157404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111171 restraints weight = 35580.312| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.19 r_work: 0.3252 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11124 Z= 0.166 Angle : 0.535 6.925 15089 Z= 0.281 Chirality : 0.043 0.154 1521 Planarity : 0.004 0.044 1987 Dihedral : 4.933 56.514 1481 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.37 % Favored : 94.56 % Rotamer: Outliers : 1.65 % Allowed : 11.38 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.22), residues: 1342 helix: 0.39 (0.29), residues: 320 sheet: -0.35 (0.32), residues: 255 loop : -1.07 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 430 TYR 0.017 0.001 TYR B 652 PHE 0.017 0.002 PHE B 130 TRP 0.010 0.001 TRP B 551 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00408 (11124) covalent geometry : angle 0.53534 (15089) hydrogen bonds : bond 0.04821 ( 355) hydrogen bonds : angle 5.98512 ( 927) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7341 (tpt) REVERT: A 307 MET cc_start: 0.7011 (mtp) cc_final: 0.5765 (mpp) REVERT: A 330 ARG cc_start: 0.7088 (ttm-80) cc_final: 0.6729 (mtm-85) REVERT: A 349 LYS cc_start: 0.7746 (mtmt) cc_final: 0.6918 (tttm) REVERT: A 359 VAL cc_start: 0.8165 (t) cc_final: 0.7706 (p) REVERT: A 418 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7343 (mtp-110) REVERT: A 585 ASP cc_start: 0.6529 (t0) cc_final: 0.6239 (t0) REVERT: A 798 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: B 126 SER cc_start: 0.8962 (p) cc_final: 0.8744 (t) REVERT: B 139 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7198 (tm-30) REVERT: B 305 SER cc_start: 0.8745 (t) cc_final: 0.8342 (m) REVERT: B 330 ARG cc_start: 0.8138 (ttp-170) cc_final: 0.7894 (ttt90) REVERT: B 423 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: B 513 LYS cc_start: 0.8523 (mttm) cc_final: 0.8277 (mtpt) REVERT: B 719 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7971 (mtmm) outliers start: 19 outliers final: 9 residues processed: 130 average time/residue: 0.9566 time to fit residues: 136.0176 Evaluate side-chains 131 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 719 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS A 167 ASN A 262 ASN B 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110929 restraints weight = 35912.414| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.24 r_work: 0.3251 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11124 Z= 0.146 Angle : 0.525 8.596 15089 Z= 0.274 Chirality : 0.042 0.153 1521 Planarity : 0.004 0.043 1987 Dihedral : 4.857 59.326 1481 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.39 % Allowed : 11.90 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.22), residues: 1342 helix: 0.50 (0.30), residues: 320 sheet: -0.30 (0.32), residues: 255 loop : -1.02 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 430 TYR 0.011 0.001 TYR A 543 PHE 0.016 0.001 PHE B 130 TRP 0.009 0.001 TRP B 551 HIS 0.006 0.001 HIS B 780 Details of bonding type rmsd covalent geometry : bond 0.00357 (11124) covalent geometry : angle 0.52476 (15089) hydrogen bonds : bond 0.04528 ( 355) hydrogen bonds : angle 5.87963 ( 927) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7327 (tpt) REVERT: A 307 MET cc_start: 0.6999 (mtp) cc_final: 0.5776 (mpp) REVERT: A 330 ARG cc_start: 0.7019 (ttm-80) cc_final: 0.6694 (mtm-85) REVERT: A 349 LYS cc_start: 0.7722 (mtmt) cc_final: 0.6889 (tttm) REVERT: A 359 VAL cc_start: 0.8220 (t) cc_final: 0.7754 (p) REVERT: A 418 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.7325 (mtp-110) REVERT: A 585 ASP cc_start: 0.6549 (t0) cc_final: 0.6213 (t0) REVERT: A 660 LYS cc_start: 0.7490 (mtpt) cc_final: 0.6976 (mtpt) REVERT: A 798 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: B 126 SER cc_start: 0.8944 (p) cc_final: 0.8742 (t) REVERT: B 139 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7179 (tm-30) REVERT: B 305 SER cc_start: 0.8739 (t) cc_final: 0.8336 (m) REVERT: B 330 ARG cc_start: 0.8133 (ttp-170) cc_final: 0.7873 (ttt90) REVERT: B 423 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: B 513 LYS cc_start: 0.8514 (mttm) cc_final: 0.8271 (mtpt) REVERT: B 719 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7982 (mtmm) REVERT: B 750 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7369 (mt-10) outliers start: 16 outliers final: 9 residues processed: 134 average time/residue: 1.0241 time to fit residues: 149.5397 Evaluate side-chains 133 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 719 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 50 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 77 optimal weight: 0.0270 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 262 ASN B 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.159708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112543 restraints weight = 35907.143| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.24 r_work: 0.3278 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11124 Z= 0.102 Angle : 0.496 8.727 15089 Z= 0.257 Chirality : 0.041 0.148 1521 Planarity : 0.004 0.041 1987 Dihedral : 4.682 58.997 1481 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.87 % Allowed : 12.42 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.23), residues: 1342 helix: 0.84 (0.30), residues: 312 sheet: -0.25 (0.32), residues: 255 loop : -0.86 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 430 TYR 0.018 0.001 TYR A 384 PHE 0.015 0.001 PHE B 130 TRP 0.007 0.001 TRP B 551 HIS 0.005 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00245 (11124) covalent geometry : angle 0.49552 (15089) hydrogen bonds : bond 0.03859 ( 355) hydrogen bonds : angle 5.73231 ( 927) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7278 (tpt) REVERT: A 307 MET cc_start: 0.6982 (mtp) cc_final: 0.5727 (mpp) REVERT: A 330 ARG cc_start: 0.6987 (ttm-80) cc_final: 0.6680 (mtm-85) REVERT: A 349 LYS cc_start: 0.7698 (mtmt) cc_final: 0.6881 (tttm) REVERT: A 359 VAL cc_start: 0.8093 (t) cc_final: 0.7635 (p) REVERT: A 418 ARG cc_start: 0.7669 (ttp-110) cc_final: 0.7307 (mtp-110) REVERT: A 585 ASP cc_start: 0.6495 (t0) cc_final: 0.6158 (t0) REVERT: A 660 LYS cc_start: 0.7486 (mtpt) cc_final: 0.6988 (mtpt) REVERT: B 139 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7183 (tm-30) REVERT: B 305 SER cc_start: 0.8677 (t) cc_final: 0.8300 (m) REVERT: B 330 ARG cc_start: 0.8072 (ttp-170) cc_final: 0.7826 (ttt90) REVERT: B 423 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7813 (mt-10) REVERT: B 513 LYS cc_start: 0.8513 (mttm) cc_final: 0.8250 (mtpt) REVERT: B 693 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7531 (pt0) REVERT: B 750 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7322 (mt-10) outliers start: 10 outliers final: 7 residues processed: 129 average time/residue: 1.0135 time to fit residues: 142.8026 Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 472 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 29 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN B 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.159182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111930 restraints weight = 35883.202| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.24 r_work: 0.3270 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11124 Z= 0.128 Angle : 0.510 9.331 15089 Z= 0.264 Chirality : 0.042 0.149 1521 Planarity : 0.004 0.041 1987 Dihedral : 4.660 57.733 1481 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.87 % Allowed : 12.42 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.23), residues: 1342 helix: 0.81 (0.30), residues: 314 sheet: -0.28 (0.32), residues: 255 loop : -0.89 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 430 TYR 0.018 0.001 TYR B 652 PHE 0.015 0.001 PHE B 130 TRP 0.009 0.001 TRP B 551 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00313 (11124) covalent geometry : angle 0.51027 (15089) hydrogen bonds : bond 0.04145 ( 355) hydrogen bonds : angle 5.71738 ( 927) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6559.98 seconds wall clock time: 111 minutes 33.66 seconds (6693.66 seconds total)