Starting phenix.real_space_refine on Wed Jun 18 09:47:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j60_61158/06_2025/9j60_61158.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j60_61158/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9j60_61158/06_2025/9j60_61158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j60_61158/06_2025/9j60_61158.map" model { file = "/net/cci-nas-00/data/ceres_data/9j60_61158/06_2025/9j60_61158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j60_61158/06_2025/9j60_61158.cif" } resolution = 2.7 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= 0.070 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.74, per 1000 atoms: 0.56 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: 5.47 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.94 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: 7.69 Time building geometry restraints manager: 6.62 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.410 Extract box with map and model: 0.910 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 47.720 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.140 ------------------------------------------------------------------------------- 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 : 3.29 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 (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: -0.84 (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 TRP 0.011 0.001 TRP B 551 HIS 0.006 0.001 HIS A 780 PHE 0.016 0.002 PHE B 402 TYR 0.019 0.002 TYR A 170 ARG 0.010 0.001 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.18822 ( 355) hydrogen bonds : angle 8.28050 ( 927) covalent geometry : bond 0.00428 (11124) covalent geometry : angle 0.62245 (15089) *********************** 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 : 1.822 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: 0.7467 (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: 2.2272 time to fit residues: 323.1273 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 : 1.574 ------------------------------------------------------------------------------- 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 113 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 0.4980 chunk 121 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.158774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111305 restraints weight = 35859.948| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.24 r_work: 0.3240 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.0703 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= 0.194 Angle : 0.557 6.875 15089 Z= 0.298 Chirality : 0.044 0.155 1521 Planarity : 0.005 0.039 1987 Dihedral : 5.256 37.790 1490 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 1.30 % Allowed : 10.43 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.68 (0.22), residues: 1342 helix: 0.26 (0.29), residues: 312 sheet: -0.12 (0.33), residues: 250 loop : -0.83 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 551 HIS 0.007 0.001 HIS A 780 PHE 0.020 0.002 PHE B 130 TYR 0.013 0.002 TYR A 543 ARG 0.004 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.05619 ( 355) hydrogen bonds : angle 6.42838 ( 927) covalent geometry : bond 0.00469 (11124) covalent geometry : angle 0.55747 (15089) *********************** 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 143 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.701 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: 0.7710 (OUTLIER) cc_final: 0.7424 (tpt) REVERT: A 307 MET cc_start: 0.6762 (mtp) cc_final: 0.5500 (mpp) REVERT: A 349 LYS cc_start: 0.7597 (mtmt) cc_final: 0.6796 (tttm) REVERT: A 418 ARG cc_start: 0.7636 (ttp-110) cc_final: 0.7289 (mtp-110) REVERT: A 585 ASP cc_start: 0.6621 (t0) cc_final: 0.6361 (t0) REVERT: A 587 GLU cc_start: 0.6578 (tp30) cc_final: 0.6370 (pt0) REVERT: A 622 MET cc_start: 0.8904 (mmm) cc_final: 0.7909 (mmt) REVERT: A 798 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: B 138 ASP cc_start: 0.7782 (t70) cc_final: 0.7547 (t70) REVERT: B 139 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7226 (tm-30) REVERT: B 330 ARG cc_start: 0.8024 (ttp-170) cc_final: 0.7716 (ttt90) outliers start: 15 outliers final: 5 residues processed: 135 average time/residue: 2.3925 time to fit residues: 351.9922 Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 1.799 ------------------------------------------------------------------------------- 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 322 ILE 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 115 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.157986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110563 restraints weight = 35914.934| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.24 r_work: 0.3238 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11124 Z= 0.192 Angle : 0.552 7.028 15089 Z= 0.292 Chirality : 0.044 0.154 1521 Planarity : 0.004 0.040 1987 Dihedral : 5.003 40.689 1483 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 1.39 % Allowed : 10.77 % 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 (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: -0.75 (0.22), residues: 1342 helix: 0.35 (0.30), residues: 312 sheet: -0.19 (0.33), residues: 251 loop : -0.95 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 551 HIS 0.007 0.001 HIS A 780 PHE 0.019 0.002 PHE B 130 TYR 0.013 0.002 TYR A 543 ARG 0.005 0.001 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.05429 ( 355) hydrogen bonds : angle 6.21038 ( 927) covalent geometry : bond 0.00468 (11124) covalent geometry : angle 0.55163 (15089) *********************** 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 141 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.581 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: 0.6852 (mtp) cc_final: 0.5543 (mpp) REVERT: A 349 LYS cc_start: 0.7650 (mtmt) cc_final: 0.6827 (tttm) REVERT: A 418 ARG cc_start: 0.7607 (ttp-110) cc_final: 0.7209 (mtp-110) REVERT: A 585 ASP cc_start: 0.6664 (t0) cc_final: 0.6422 (t0) REVERT: A 622 MET cc_start: 0.8880 (mmm) cc_final: 0.8044 (mmt) REVERT: A 660 LYS cc_start: 0.7314 (mtpt) cc_final: 0.6687 (mtpt) REVERT: A 798 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: B 139 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7258 (tm-30) REVERT: B 305 SER cc_start: 0.8696 (t) cc_final: 0.8308 (m) REVERT: B 330 ARG cc_start: 0.8098 (ttp-170) cc_final: 0.7825 (ttt90) REVERT: B 719 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8022 (mtmm) outliers start: 16 outliers final: 8 residues processed: 135 average time/residue: 2.2930 time to fit residues: 338.3938 Evaluate side-chains 130 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 605 SER 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 322 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 719 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 101 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 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 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN B 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111085 restraints weight = 36244.184| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.26 r_work: 0.3237 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1192 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= 0.152 Angle : 0.522 7.168 15089 Z= 0.275 Chirality : 0.043 0.153 1521 Planarity : 0.004 0.041 1987 Dihedral : 4.897 43.565 1483 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.16 % Rotamer: Outliers : 1.39 % Allowed : 11.12 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.68 (0.22), residues: 1342 helix: 0.51 (0.30), residues: 311 sheet: -0.25 (0.32), residues: 254 loop : -0.91 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 551 HIS 0.008 0.001 HIS A 158 PHE 0.017 0.001 PHE B 130 TYR 0.013 0.001 TYR B 652 ARG 0.003 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04801 ( 355) hydrogen bonds : angle 6.03742 ( 927) covalent geometry : bond 0.00372 (11124) covalent geometry : angle 0.52219 (15089) *********************** 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 136 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.819 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: A 168 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7395 (tpt) REVERT: A 307 MET cc_start: 0.6876 (mtp) cc_final: 0.5565 (mpp) REVERT: A 349 LYS cc_start: 0.7683 (mtmt) cc_final: 0.6891 (tttm) REVERT: A 418 ARG cc_start: 0.7649 (ttp-110) cc_final: 0.7256 (mtp-110) REVERT: A 585 ASP cc_start: 0.6585 (t0) cc_final: 0.6314 (t0) REVERT: A 622 MET cc_start: 0.8832 (mmm) cc_final: 0.8068 (mmt) REVERT: A 660 LYS cc_start: 0.7324 (mtpt) cc_final: 0.6475 (mtpt) REVERT: A 798 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: B 126 SER cc_start: 0.9029 (p) cc_final: 0.8800 (t) REVERT: B 139 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7269 (tm-30) REVERT: B 305 SER cc_start: 0.8683 (t) cc_final: 0.8304 (m) REVERT: B 330 ARG cc_start: 0.8089 (ttp-170) cc_final: 0.7817 (ttt90) REVERT: B 423 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: B 513 LYS cc_start: 0.8532 (mttm) cc_final: 0.8283 (mtpt) REVERT: B 719 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8001 (mtmm) outliers start: 16 outliers final: 7 residues processed: 130 average time/residue: 2.2842 time to fit residues: 325.8884 Evaluate side-chains 131 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 423 GLU 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 21 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.157427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110158 restraints weight = 36197.329| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.24 r_work: 0.3222 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11124 Z= 0.198 Angle : 0.553 7.862 15089 Z= 0.292 Chirality : 0.044 0.156 1521 Planarity : 0.005 0.043 1987 Dihedral : 5.000 48.175 1483 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.41 % Rotamer: Outliers : 1.91 % Allowed : 10.77 % 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 (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 (0.22), residues: 1342 helix: 0.39 (0.30), residues: 312 sheet: -0.20 (0.33), residues: 250 loop : -1.04 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 551 HIS 0.007 0.002 HIS A 362 PHE 0.019 0.002 PHE B 130 TYR 0.015 0.002 TYR B 652 ARG 0.003 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.05217 ( 355) hydrogen bonds : angle 6.03945 ( 927) covalent geometry : bond 0.00485 (11124) covalent geometry : angle 0.55325 (15089) *********************** 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 140 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.578 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: 0.7391 (tt0) cc_final: 0.7058 (tt0) REVERT: A 168 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7463 (tpt) REVERT: A 307 MET cc_start: 0.6897 (mtp) cc_final: 0.5617 (mpp) REVERT: A 349 LYS cc_start: 0.7680 (mtmt) cc_final: 0.6858 (tttm) REVERT: A 418 ARG cc_start: 0.7639 (ttp-110) cc_final: 0.7240 (mtp-110) REVERT: A 585 ASP cc_start: 0.6626 (t0) cc_final: 0.6374 (t0) REVERT: A 622 MET cc_start: 0.8808 (mmm) cc_final: 0.8222 (mmt) REVERT: A 798 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: B 139 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7277 (tm-30) REVERT: B 305 SER cc_start: 0.8719 (t) cc_final: 0.8335 (m) REVERT: B 330 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7889 (ttt90) REVERT: B 423 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7900 (mt-10) REVERT: B 513 LYS cc_start: 0.8566 (mttm) cc_final: 0.8311 (mtpt) REVERT: B 719 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7994 (mtmm) outliers start: 22 outliers final: 9 residues processed: 134 average time/residue: 2.4114 time to fit residues: 353.2554 Evaluate side-chains 130 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 605 SER 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 379 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 620 SER 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 57 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 0.0980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.159657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112575 restraints weight = 35844.962| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.23 r_work: 0.3269 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11124 Z= 0.101 Angle : 0.490 7.554 15089 Z= 0.256 Chirality : 0.041 0.148 1521 Planarity : 0.004 0.041 1987 Dihedral : 4.721 49.592 1483 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.04 % Allowed : 11.56 % 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 (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: -0.56 (0.23), residues: 1342 helix: 0.72 (0.30), residues: 318 sheet: -0.27 (0.32), residues: 254 loop : -0.85 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 551 HIS 0.006 0.001 HIS A 362 PHE 0.014 0.001 PHE B 130 TYR 0.015 0.001 TYR B 652 ARG 0.002 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 355) hydrogen bonds : angle 5.82462 ( 927) covalent geometry : bond 0.00241 (11124) covalent geometry : angle 0.49029 (15089) *********************** 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 138 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 1.866 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: A 162 GLU cc_start: 0.7386 (tt0) cc_final: 0.7106 (tt0) REVERT: A 307 MET cc_start: 0.6862 (mtp) cc_final: 0.5604 (mpp) REVERT: A 330 ARG cc_start: 0.6918 (ttm-80) cc_final: 0.6613 (mtm-85) REVERT: A 349 LYS cc_start: 0.7660 (mtmt) cc_final: 0.6881 (tttm) REVERT: A 418 ARG cc_start: 0.7675 (ttp-110) cc_final: 0.7301 (mtp-110) REVERT: A 585 ASP cc_start: 0.6633 (t0) cc_final: 0.6343 (t0) REVERT: A 622 MET cc_start: 0.8725 (mmm) cc_final: 0.7966 (mmt) REVERT: A 660 LYS cc_start: 0.7241 (mtpt) cc_final: 0.6721 (mtpt) REVERT: B 100 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7893 (mmm) REVERT: B 126 SER cc_start: 0.9013 (p) cc_final: 0.8802 (t) REVERT: B 139 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7225 (tm-30) REVERT: B 305 SER cc_start: 0.8678 (t) cc_final: 0.8311 (m) REVERT: B 330 ARG cc_start: 0.8096 (ttp-170) cc_final: 0.7852 (ttt90) REVERT: B 513 LYS cc_start: 0.8504 (mttm) cc_final: 0.8224 (mtpt) outliers start: 12 outliers final: 7 residues processed: 133 average time/residue: 2.3288 time to fit residues: 338.5006 Evaluate side-chains 128 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 472 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 105 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3909 r_free = 0.3909 target = 0.159138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112125 restraints weight = 36099.039| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.24 r_work: 0.3268 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1591 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= 0.132 Angle : 0.507 7.693 15089 Z= 0.264 Chirality : 0.042 0.150 1521 Planarity : 0.004 0.040 1987 Dihedral : 4.728 50.695 1483 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.30 % Allowed : 11.82 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.55 (0.23), residues: 1342 helix: 0.74 (0.30), residues: 318 sheet: -0.27 (0.33), residues: 254 loop : -0.86 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 551 HIS 0.005 0.001 HIS A 780 PHE 0.016 0.001 PHE B 130 TYR 0.011 0.001 TYR A 543 ARG 0.007 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 355) hydrogen bonds : angle 5.83088 ( 927) covalent geometry : bond 0.00324 (11124) covalent geometry : angle 0.50653 (15089) *********************** 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 134 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.590 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 100 MET cc_start: 0.7487 (mpp) cc_final: 0.7238 (mpp) REVERT: A 162 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7093 (tt0) REVERT: A 307 MET cc_start: 0.6898 (mtp) cc_final: 0.5614 (mpp) REVERT: A 316 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8462 (t0) REVERT: A 330 ARG cc_start: 0.6903 (ttm-80) cc_final: 0.6497 (mtm-85) REVERT: A 349 LYS cc_start: 0.7664 (mtmt) cc_final: 0.6876 (tttm) REVERT: A 418 ARG cc_start: 0.7664 (ttp-110) cc_final: 0.7295 (mtp-110) REVERT: A 585 ASP cc_start: 0.6609 (t0) cc_final: 0.6279 (t0) REVERT: A 622 MET cc_start: 0.8735 (mmm) cc_final: 0.7953 (mmt) REVERT: A 660 LYS cc_start: 0.7278 (mtpt) cc_final: 0.6777 (mtpt) REVERT: B 100 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7871 (mmm) REVERT: B 139 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7212 (tm-30) REVERT: B 305 SER cc_start: 0.8667 (t) cc_final: 0.8309 (m) REVERT: B 330 ARG cc_start: 0.8096 (ttp-170) cc_final: 0.7862 (ttt90) REVERT: B 513 LYS cc_start: 0.8503 (mttm) cc_final: 0.8254 (mtpt) REVERT: B 719 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7973 (mtmm) outliers start: 15 outliers final: 8 residues processed: 128 average time/residue: 2.3051 time to fit residues: 322.9488 Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain B residue 100 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 115 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 166 HIS A 167 ASN A 262 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.158595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111698 restraints weight = 35899.020| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.23 r_work: 0.3259 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11124 Z= 0.144 Angle : 0.514 7.652 15089 Z= 0.269 Chirality : 0.042 0.151 1521 Planarity : 0.004 0.041 1987 Dihedral : 4.790 53.241 1483 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.74 % Allowed : 11.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1342 helix: 0.70 (0.30), residues: 319 sheet: -0.32 (0.32), residues: 255 loop : -0.88 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 507 HIS 0.006 0.001 HIS A 780 PHE 0.016 0.001 PHE B 130 TYR 0.012 0.001 TYR A 543 ARG 0.006 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 355) hydrogen bonds : angle 5.83879 ( 927) covalent geometry : bond 0.00353 (11124) covalent geometry : angle 0.51385 (15089) *********************** 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: 20 poor density : 118 time to evaluate : 1.812 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: A 162 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: A 307 MET cc_start: 0.6917 (mtp) cc_final: 0.5637 (mpp) REVERT: A 330 ARG cc_start: 0.6971 (ttm-80) cc_final: 0.6607 (mtm-85) REVERT: A 349 LYS cc_start: 0.7646 (mtmt) cc_final: 0.6844 (tttm) REVERT: A 418 ARG cc_start: 0.7660 (ttp-110) cc_final: 0.7297 (mtp-110) REVERT: A 585 ASP cc_start: 0.6572 (t0) cc_final: 0.6271 (t0) REVERT: A 622 MET cc_start: 0.8756 (mmm) cc_final: 0.8106 (mmt) REVERT: A 660 LYS cc_start: 0.7304 (mtpt) cc_final: 0.6838 (mtpt) REVERT: A 798 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: B 139 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7182 (tm-30) REVERT: B 305 SER cc_start: 0.8661 (t) cc_final: 0.8312 (m) REVERT: B 330 ARG cc_start: 0.8129 (ttp-170) cc_final: 0.7866 (ttt90) REVERT: B 513 LYS cc_start: 0.8504 (mttm) cc_final: 0.8259 (mtpt) REVERT: B 719 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7970 (mtmm) outliers start: 20 outliers final: 10 residues processed: 129 average time/residue: 2.2718 time to fit residues: 321.2133 Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 605 SER 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 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 12 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 120 optimal weight: 0.1980 chunk 0 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 A 316 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.159596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.112599 restraints weight = 35896.471| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.22 r_work: 0.3264 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11124 Z= 0.116 Angle : 0.503 8.603 15089 Z= 0.261 Chirality : 0.041 0.148 1521 Planarity : 0.004 0.040 1987 Dihedral : 4.700 54.381 1483 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.30 % Allowed : 12.08 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.46 (0.23), residues: 1342 helix: 0.95 (0.30), residues: 312 sheet: -0.27 (0.32), residues: 254 loop : -0.83 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 507 HIS 0.004 0.001 HIS A 780 PHE 0.015 0.001 PHE B 130 TYR 0.017 0.001 TYR B 652 ARG 0.006 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 355) hydrogen bonds : angle 5.73573 ( 927) covalent geometry : bond 0.00282 (11124) covalent geometry : angle 0.50286 (15089) *********************** 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 134 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.623 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: A 162 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7110 (tt0) REVERT: A 307 MET cc_start: 0.6905 (mtp) cc_final: 0.5614 (mpp) REVERT: A 330 ARG cc_start: 0.6920 (ttm-80) cc_final: 0.6553 (mtm-85) REVERT: A 349 LYS cc_start: 0.7638 (mtmt) cc_final: 0.6835 (tttm) REVERT: A 418 ARG cc_start: 0.7667 (ttp-110) cc_final: 0.7304 (mtp-110) REVERT: A 585 ASP cc_start: 0.6535 (t0) cc_final: 0.6220 (t0) REVERT: A 622 MET cc_start: 0.8727 (mmm) cc_final: 0.7993 (mmt) REVERT: A 660 LYS cc_start: 0.7313 (mtpt) cc_final: 0.6858 (mtpt) REVERT: A 798 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: B 139 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7206 (tm-30) REVERT: B 305 SER cc_start: 0.8639 (t) cc_final: 0.8300 (m) REVERT: B 330 ARG cc_start: 0.8112 (ttp-170) cc_final: 0.7861 (ttt90) REVERT: B 513 LYS cc_start: 0.8510 (mttm) cc_final: 0.8252 (mtpt) REVERT: B 719 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7962 (mtmm) REVERT: B 750 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7322 (mt-10) outliers start: 15 outliers final: 9 residues processed: 127 average time/residue: 2.3053 time to fit residues: 322.8073 Evaluate side-chains 128 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 605 SER 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 472 ASP Chi-restraints excluded: chain B residue 525 THR 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 43 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.158751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111693 restraints weight = 35995.932| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.24 r_work: 0.3260 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1820 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= 0.150 Angle : 0.525 9.280 15089 Z= 0.273 Chirality : 0.042 0.152 1521 Planarity : 0.004 0.041 1987 Dihedral : 4.777 56.025 1483 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.04 % Allowed : 12.42 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1342 helix: 0.82 (0.30), residues: 314 sheet: -0.34 (0.32), residues: 255 loop : -0.92 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 551 HIS 0.006 0.001 HIS A 780 PHE 0.016 0.002 PHE B 130 TYR 0.018 0.001 TYR B 652 ARG 0.006 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 355) hydrogen bonds : angle 5.80116 ( 927) covalent geometry : bond 0.00368 (11124) covalent geometry : angle 0.52500 (15089) ********************** 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 133 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.696 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: 0.7462 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: A 307 MET cc_start: 0.6925 (mtp) cc_final: 0.5651 (mpp) REVERT: A 330 ARG cc_start: 0.6936 (ttm-80) cc_final: 0.6568 (mtm-85) REVERT: A 349 LYS cc_start: 0.7663 (mtmt) cc_final: 0.6852 (tttm) REVERT: A 418 ARG cc_start: 0.7670 (ttp-110) cc_final: 0.7307 (mtp-110) REVERT: A 585 ASP cc_start: 0.6527 (t0) cc_final: 0.6205 (t0) REVERT: A 660 LYS cc_start: 0.7332 (mtpt) cc_final: 0.6886 (mtpt) REVERT: A 798 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: B 139 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7171 (tm-30) REVERT: B 305 SER cc_start: 0.8670 (t) cc_final: 0.8333 (m) REVERT: B 330 ARG cc_start: 0.8119 (ttp-170) cc_final: 0.7845 (ttt90) REVERT: B 513 LYS cc_start: 0.8526 (mttm) cc_final: 0.8272 (mtpt) REVERT: B 719 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7966 (mtmm) REVERT: B 750 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7347 (mt-10) outliers start: 12 outliers final: 9 residues processed: 128 average time/residue: 2.3981 time to fit residues: 335.9655 Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 605 SER 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 472 ASP Chi-restraints excluded: chain B residue 525 THR 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 11 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.109218 restraints weight = 36141.950| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.25 r_work: 0.3222 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11124 Z= 0.227 Angle : 0.580 9.404 15089 Z= 0.305 Chirality : 0.045 0.157 1521 Planarity : 0.005 0.044 1987 Dihedral : 5.031 59.747 1483 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.30 % Allowed : 12.42 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.88 (0.22), residues: 1342 helix: 0.43 (0.29), residues: 320 sheet: -0.41 (0.32), residues: 255 loop : -1.08 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 551 HIS 0.007 0.002 HIS A 780 PHE 0.018 0.002 PHE B 130 TYR 0.015 0.002 TYR A 543 ARG 0.010 0.001 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.05343 ( 355) hydrogen bonds : angle 5.98895 ( 927) covalent geometry : bond 0.00558 (11124) covalent geometry : angle 0.58029 (15089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14276.28 seconds wall clock time: 242 minutes 49.85 seconds (14569.85 seconds total)