Starting phenix.real_space_refine on Wed Feb 4 13:08:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qip_53193/02_2026/9qip_53193_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qip_53193/02_2026/9qip_53193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qip_53193/02_2026/9qip_53193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qip_53193/02_2026/9qip_53193.map" model { file = "/net/cci-nas-00/data/ceres_data/9qip_53193/02_2026/9qip_53193_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qip_53193/02_2026/9qip_53193_neut.cif" } resolution = 4.15 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= -0.001 sd= 0.027 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 P 9 5.49 5 S 50 5.16 5 C 6623 2.51 5 N 1760 2.21 5 O 1991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10433 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2346 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 275} Chain: "B" Number of atoms: 8020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8020 Classifications: {'peptide': 1012} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 50, 'TRANS': 956} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'ATP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.36, per 1000 atoms: 0.23 Number of scatterers: 10433 At special positions: 0 Unit cell: (80.85, 104.775, 136.125, 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 50 16.00 P 9 15.00 O 1991 8.00 N 1760 7.00 C 6623 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 539.5 milliseconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2484 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 49.8% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 4522 through 4534 removed outlier: 4.280A pdb=" N LYS A4534 " --> pdb=" O ALA A4530 " (cutoff:3.500A) Processing helix chain 'A' and resid 4559 through 4565 Processing helix chain 'A' and resid 4571 through 4588 removed outlier: 3.579A pdb=" N ALA A4575 " --> pdb=" O SER A4571 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A4583 " --> pdb=" O ALA A4579 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR A4584 " --> pdb=" O GLN A4580 " (cutoff:3.500A) Processing helix chain 'A' and resid 4676 through 4680 Processing helix chain 'A' and resid 4687 through 4699 removed outlier: 3.588A pdb=" N GLN A4696 " --> pdb=" O LEU A4692 " (cutoff:3.500A) Processing helix chain 'A' and resid 4704 through 4708 Processing helix chain 'A' and resid 4717 through 4738 Processing helix chain 'A' and resid 4740 through 4746 Processing helix chain 'A' and resid 4748 through 4750 No H-bonds generated for 'chain 'A' and resid 4748 through 4750' Processing helix chain 'A' and resid 4751 through 4782 removed outlier: 5.265A pdb=" N VAL A4764 " --> pdb=" O TYR A4760 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU A4765 " --> pdb=" O LEU A4761 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A4766 " --> pdb=" O LYS A4762 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A4768 " --> pdb=" O VAL A4764 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU A4771 " --> pdb=" O MET A4767 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER A4782 " --> pdb=" O GLN A4778 " (cutoff:3.500A) Processing helix chain 'A' and resid 4786 through 4811 removed outlier: 3.780A pdb=" N HIS A4792 " --> pdb=" O ARG A4788 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 7.109A pdb=" N ARG B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLN B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.530A pdb=" N MET B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.650A pdb=" N GLY B 102 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 117 through 130 removed outlier: 4.706A pdb=" N LYS B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N HIS B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 129 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 154 removed outlier: 3.566A pdb=" N LYS B 153 " --> pdb=" O PHE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 177 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.811A pdb=" N LYS B 307 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 340 Processing helix chain 'B' and resid 347 through 365 Processing helix chain 'B' and resid 372 through 382 Processing helix chain 'B' and resid 387 through 406 Processing helix chain 'B' and resid 421 through 427 removed outlier: 4.460A pdb=" N VAL B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 421 through 427' Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 443 through 451 removed outlier: 3.546A pdb=" N CYS B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 520 through 533 removed outlier: 4.055A pdb=" N LYS B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 552 removed outlier: 4.124A pdb=" N THR B 551 " --> pdb=" O THR B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 570 through 585 removed outlier: 3.700A pdb=" N ARG B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 614 Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 633 through 650 Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 681 through 691 Processing helix chain 'B' and resid 695 through 712 Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 751 through 769 Processing helix chain 'B' and resid 774 through 778 Processing helix chain 'B' and resid 779 through 789 removed outlier: 4.251A pdb=" N GLU B 789 " --> pdb=" O ASN B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 834 Processing helix chain 'B' and resid 857 through 873 Processing helix chain 'B' and resid 879 through 889 Processing helix chain 'B' and resid 894 through 914 Processing helix chain 'B' and resid 917 through 920 Processing helix chain 'B' and resid 967 through 979 Processing helix chain 'B' and resid 1002 through 1007 Processing helix chain 'B' and resid 1008 through 1014 Processing sheet with id=AA1, first strand: chain 'A' and resid 4537 through 4539 removed outlier: 3.710A pdb=" N CYS A4601 " --> pdb=" O ASP A4538 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4543 through 4545 Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 138 removed outlier: 6.426A pdb=" N VAL B 88 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N SER B 138 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE B 90 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 64 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N HIS B 91 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B 66 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS B 156 " --> pdb=" O HIS B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AA5, first strand: chain 'B' and resid 260 through 262 removed outlier: 4.437A pdb=" N PHE B 244 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE B 250 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLY B 285 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY B 286 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N SER B 272 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL B 265 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 538 through 541 removed outlier: 6.300A pdb=" N ILE B 493 " --> pdb=" O ASP B 539 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N HIS B 541 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 495 " --> pdb=" O HIS B 541 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN B 462 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ILE B 565 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE B 464 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER B 591 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS B 924 " --> pdb=" O THR B 600 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL B 602 " --> pdb=" O LYS B 922 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LYS B 922 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 944 through 947 removed outlier: 6.768A pdb=" N ILE B 950 " --> pdb=" O ILE B 946 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.726A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B1027 " --> pdb=" O MET B 985 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET B 985 " --> pdb=" O SER B1027 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLN B 988 " --> pdb=" O MET B 992 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N MET B 992 " --> pdb=" O GLN B 988 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.726A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3394 1.34 - 1.46: 2287 1.46 - 1.58: 4910 1.58 - 1.70: 11 1.70 - 1.81: 73 Bond restraints: 10675 Sorted by residual: bond pdb=" N GLY B 962 " pdb=" CA GLY B 962 " ideal model delta sigma weight residual 1.458 1.443 0.015 9.20e-03 1.18e+04 2.58e+00 bond pdb=" C VAL B 997 " pdb=" N MET B 998 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.47e-02 4.63e+03 1.99e+00 bond pdb=" C ASN A4682 " pdb=" O ASN A4682 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.75e+00 bond pdb=" CA LYS B1014 " pdb=" CB LYS B1014 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.40e+00 bond pdb=" CD GLU B 908 " pdb=" OE1 GLU B 908 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.33e+00 ... (remaining 10670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 14318 2.22 - 4.45: 156 4.45 - 6.67: 13 6.67 - 8.89: 2 8.89 - 11.12: 2 Bond angle restraints: 14491 Sorted by residual: angle pdb=" N GLU B 908 " pdb=" CA GLU B 908 " pdb=" CB GLU B 908 " ideal model delta sigma weight residual 110.28 116.91 -6.63 1.55e+00 4.16e-01 1.83e+01 angle pdb=" N PHE B 106 " pdb=" CA PHE B 106 " pdb=" C PHE B 106 " ideal model delta sigma weight residual 114.56 109.46 5.10 1.27e+00 6.20e-01 1.61e+01 angle pdb=" N ALA B 632 " pdb=" CA ALA B 632 " pdb=" C ALA B 632 " ideal model delta sigma weight residual 114.56 110.02 4.54 1.27e+00 6.20e-01 1.28e+01 angle pdb=" CB MET A4542 " pdb=" CG MET A4542 " pdb=" SD MET A4542 " ideal model delta sigma weight residual 112.70 122.81 -10.11 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CA LEU B 828 " pdb=" CB LEU B 828 " pdb=" CG LEU B 828 " ideal model delta sigma weight residual 116.30 127.42 -11.12 3.50e+00 8.16e-02 1.01e+01 ... (remaining 14486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 6005 16.97 - 33.94: 397 33.94 - 50.91: 79 50.91 - 67.88: 21 67.88 - 84.85: 11 Dihedral angle restraints: 6513 sinusoidal: 2689 harmonic: 3824 Sorted by residual: dihedral pdb=" CA PHE A4598 " pdb=" C PHE A4598 " pdb=" N VAL A4599 " pdb=" CA VAL A4599 " ideal model delta harmonic sigma weight residual -180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TYR A4621 " pdb=" C TYR A4621 " pdb=" N ALA A4622 " pdb=" CA ALA A4622 " ideal model delta harmonic sigma weight residual -180.00 -162.64 -17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA VAL A4653 " pdb=" C VAL A4653 " pdb=" N ARG A4654 " pdb=" CA ARG A4654 " ideal model delta harmonic sigma weight residual 180.00 163.61 16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 6510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1092 0.033 - 0.066: 360 0.066 - 0.100: 112 0.100 - 0.133: 52 0.133 - 0.166: 3 Chirality restraints: 1619 Sorted by residual: chirality pdb=" CB ILE B 221 " pdb=" CA ILE B 221 " pdb=" CG1 ILE B 221 " pdb=" CG2 ILE B 221 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CA GLU B 908 " pdb=" N GLU B 908 " pdb=" C GLU B 908 " pdb=" CB GLU B 908 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CB ILE B 946 " pdb=" CA ILE B 946 " pdb=" CG1 ILE B 946 " pdb=" CG2 ILE B 946 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 1616 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 497 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 498 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 498 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 498 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 267 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO B 268 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A4656 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A4657 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A4657 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A4657 " 0.021 5.00e-02 4.00e+02 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3539 2.86 - 3.37: 11092 3.37 - 3.88: 18720 3.88 - 4.39: 21188 4.39 - 4.90: 34142 Nonbonded interactions: 88681 Sorted by model distance: nonbonded pdb=" O LEU B 904 " pdb=" OE1 GLU B 908 " model vdw 2.348 3.040 nonbonded pdb=" O ALA B 422 " pdb=" OE1 GLU B 426 " model vdw 2.599 3.040 nonbonded pdb=" N ASP A4607 " pdb=" OD1 ASP A4607 " model vdw 2.606 3.120 nonbonded pdb=" O2' ATP B1102 " pdb=" O3' ATP B1102 " model vdw 2.614 2.432 nonbonded pdb=" N SER B 267 " pdb=" O SER B 267 " model vdw 2.627 2.496 ... (remaining 88676 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.260 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 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 : 0.002 0.034 10675 Z= 0.131 Angle : 0.595 11.116 14491 Z= 0.342 Chirality : 0.040 0.166 1619 Planarity : 0.004 0.045 1858 Dihedral : 12.747 84.847 4029 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.16 (0.24), residues: 1301 helix: 1.25 (0.22), residues: 574 sheet: 0.37 (0.39), residues: 181 loop : 0.59 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4574 TYR 0.014 0.001 TYR A4528 PHE 0.019 0.001 PHE B 656 TRP 0.012 0.001 TRP B 416 HIS 0.008 0.001 HIS A4558 Details of bonding type rmsd covalent geometry : bond 0.00243 (10675) covalent geometry : angle 0.59546 (14491) hydrogen bonds : bond 0.14092 ( 503) hydrogen bonds : angle 6.70032 ( 1392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4612 LEU cc_start: 0.9775 (tp) cc_final: 0.9421 (tp) REVERT: A 4625 CYS cc_start: 0.9687 (m) cc_final: 0.9180 (t) REVERT: A 4767 MET cc_start: 0.9548 (ptp) cc_final: 0.8992 (mmt) REVERT: B 56 MET cc_start: 0.9527 (mtm) cc_final: 0.9229 (mtt) REVERT: B 59 MET cc_start: 0.9465 (ttt) cc_final: 0.8779 (tmm) REVERT: B 69 MET cc_start: 0.9080 (mmm) cc_final: 0.7836 (mmm) REVERT: B 403 LEU cc_start: 0.9842 (mt) cc_final: 0.9602 (mt) REVERT: B 461 LEU cc_start: 0.9420 (mt) cc_final: 0.9210 (mt) REVERT: B 475 MET cc_start: 0.9415 (mmm) cc_final: 0.9207 (mmm) REVERT: B 844 MET cc_start: 0.8300 (ppp) cc_final: 0.7496 (ppp) REVERT: B 1009 MET cc_start: 0.9128 (mmp) cc_final: 0.8585 (mmm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0809 time to fit residues: 7.7452 Evaluate side-chains 48 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4758 HIS ** A4793 HIS ** 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 = 0.2629 r_free = 0.2629 target = 0.025046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.018681 restraints weight = 116195.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.019400 restraints weight = 74387.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.019922 restraints weight = 53850.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.020340 restraints weight = 42206.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.020632 restraints weight = 34898.452| |-----------------------------------------------------------------------------| r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10675 Z= 0.150 Angle : 0.519 6.410 14491 Z= 0.278 Chirality : 0.039 0.142 1619 Planarity : 0.004 0.040 1858 Dihedral : 6.656 64.911 1469 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.09 % Allowed : 1.56 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.27 (0.24), residues: 1301 helix: 1.37 (0.22), residues: 563 sheet: 0.71 (0.40), residues: 166 loop : 0.50 (0.29), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4574 TYR 0.017 0.001 TYR A4528 PHE 0.016 0.002 PHE A4598 TRP 0.008 0.001 TRP B 660 HIS 0.006 0.001 HIS A4558 Details of bonding type rmsd covalent geometry : bond 0.00301 (10675) covalent geometry : angle 0.51878 (14491) hydrogen bonds : bond 0.04204 ( 503) hydrogen bonds : angle 5.23879 ( 1392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4612 LEU cc_start: 0.9741 (tp) cc_final: 0.9462 (tp) REVERT: A 4625 CYS cc_start: 0.9688 (m) cc_final: 0.8996 (m) REVERT: A 4628 PHE cc_start: 0.9666 (m-80) cc_final: 0.9337 (m-80) REVERT: A 4740 MET cc_start: 0.9773 (mtt) cc_final: 0.9438 (mmm) REVERT: A 4767 MET cc_start: 0.9540 (ptp) cc_final: 0.8806 (mmt) REVERT: B 56 MET cc_start: 0.9512 (mtm) cc_final: 0.9257 (mtt) REVERT: B 59 MET cc_start: 0.9450 (ttt) cc_final: 0.8766 (tmm) REVERT: B 69 MET cc_start: 0.9274 (mmm) cc_final: 0.8799 (mmm) REVERT: B 162 MET cc_start: 0.9330 (tpt) cc_final: 0.8770 (mmm) REVERT: B 403 LEU cc_start: 0.9872 (mt) cc_final: 0.9658 (mt) REVERT: B 461 LEU cc_start: 0.9415 (mt) cc_final: 0.9140 (mt) REVERT: B 475 MET cc_start: 0.9404 (mmm) cc_final: 0.9197 (mmm) REVERT: B 844 MET cc_start: 0.8413 (ppp) cc_final: 0.7469 (ppp) REVERT: B 1009 MET cc_start: 0.9232 (mmp) cc_final: 0.8862 (mmm) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.0739 time to fit residues: 6.6888 Evaluate side-chains 46 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 0.0670 chunk 61 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4792 HIS ** A4793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.024803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.018532 restraints weight = 119038.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2372 r_free = 0.2372 target = 0.019247 restraints weight = 75817.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.019763 restraints weight = 54756.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.020164 restraints weight = 42869.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.020472 restraints weight = 35440.985| |-----------------------------------------------------------------------------| r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10675 Z= 0.168 Angle : 0.522 6.944 14491 Z= 0.280 Chirality : 0.039 0.141 1619 Planarity : 0.004 0.037 1858 Dihedral : 6.613 70.169 1469 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.09 % Allowed : 2.68 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.34 (0.24), residues: 1301 helix: 1.45 (0.22), residues: 567 sheet: 0.51 (0.39), residues: 175 loop : 0.61 (0.29), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 175 TYR 0.014 0.001 TYR A4528 PHE 0.015 0.002 PHE B 656 TRP 0.009 0.001 TRP B 660 HIS 0.006 0.001 HIS A4558 Details of bonding type rmsd covalent geometry : bond 0.00336 (10675) covalent geometry : angle 0.52164 (14491) hydrogen bonds : bond 0.03965 ( 503) hydrogen bonds : angle 4.97961 ( 1392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4612 LEU cc_start: 0.9761 (tp) cc_final: 0.9500 (tp) REVERT: A 4625 CYS cc_start: 0.9672 (m) cc_final: 0.9009 (m) REVERT: A 4628 PHE cc_start: 0.9658 (m-80) cc_final: 0.9381 (m-80) REVERT: A 4740 MET cc_start: 0.9774 (mtt) cc_final: 0.9455 (mmm) REVERT: A 4767 MET cc_start: 0.9513 (ptp) cc_final: 0.9054 (mmm) REVERT: B 56 MET cc_start: 0.9508 (mtm) cc_final: 0.9291 (mtt) REVERT: B 59 MET cc_start: 0.9459 (ttt) cc_final: 0.8794 (tmm) REVERT: B 69 MET cc_start: 0.9391 (mmm) cc_final: 0.8891 (mmm) REVERT: B 162 MET cc_start: 0.9244 (tpt) cc_final: 0.8782 (mmm) REVERT: B 403 LEU cc_start: 0.9868 (mt) cc_final: 0.9647 (mt) REVERT: B 461 LEU cc_start: 0.9385 (mt) cc_final: 0.9138 (mt) REVERT: B 844 MET cc_start: 0.8566 (ppp) cc_final: 0.7678 (ppp) REVERT: B 1009 MET cc_start: 0.9230 (mmp) cc_final: 0.8848 (mmm) outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.0794 time to fit residues: 6.9656 Evaluate side-chains 45 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 41 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.024806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2342 r_free = 0.2342 target = 0.018558 restraints weight = 119176.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.019260 restraints weight = 75981.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.019781 restraints weight = 55063.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.020182 restraints weight = 43149.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.020485 restraints weight = 35688.658| |-----------------------------------------------------------------------------| r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10675 Z= 0.158 Angle : 0.512 7.131 14491 Z= 0.273 Chirality : 0.039 0.210 1619 Planarity : 0.004 0.037 1858 Dihedral : 6.518 69.373 1469 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.34 (0.24), residues: 1301 helix: 1.47 (0.22), residues: 567 sheet: 0.59 (0.39), residues: 177 loop : 0.54 (0.29), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 175 TYR 0.014 0.001 TYR A4528 PHE 0.015 0.001 PHE B 656 TRP 0.008 0.001 TRP B 660 HIS 0.006 0.001 HIS A4558 Details of bonding type rmsd covalent geometry : bond 0.00319 (10675) covalent geometry : angle 0.51187 (14491) hydrogen bonds : bond 0.03726 ( 503) hydrogen bonds : angle 4.81514 ( 1392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4532 MET cc_start: 0.9496 (mpp) cc_final: 0.8956 (mtt) REVERT: A 4612 LEU cc_start: 0.9769 (tp) cc_final: 0.9519 (tp) REVERT: A 4625 CYS cc_start: 0.9650 (m) cc_final: 0.8957 (m) REVERT: A 4628 PHE cc_start: 0.9616 (m-80) cc_final: 0.9343 (m-80) REVERT: A 4740 MET cc_start: 0.9763 (mtt) cc_final: 0.9453 (mmm) REVERT: A 4767 MET cc_start: 0.9493 (ptp) cc_final: 0.9073 (mmm) REVERT: B 56 MET cc_start: 0.9489 (mtm) cc_final: 0.9077 (mtt) REVERT: B 59 MET cc_start: 0.9461 (ttt) cc_final: 0.8807 (tmm) REVERT: B 162 MET cc_start: 0.9191 (tpt) cc_final: 0.8736 (mmm) REVERT: B 403 LEU cc_start: 0.9865 (mt) cc_final: 0.9651 (mt) REVERT: B 461 LEU cc_start: 0.9354 (mt) cc_final: 0.9095 (mt) REVERT: B 475 MET cc_start: 0.9767 (mmp) cc_final: 0.9433 (mmm) REVERT: B 844 MET cc_start: 0.8653 (ppp) cc_final: 0.7777 (ppp) REVERT: B 1009 MET cc_start: 0.9221 (mmp) cc_final: 0.8847 (mmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0761 time to fit residues: 6.9517 Evaluate side-chains 43 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 27 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 119 optimal weight: 0.0470 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.025195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.018863 restraints weight = 116775.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.019584 restraints weight = 74482.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.020127 restraints weight = 53861.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.020537 restraints weight = 42161.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.020855 restraints weight = 34802.056| |-----------------------------------------------------------------------------| r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10675 Z= 0.114 Angle : 0.486 7.533 14491 Z= 0.258 Chirality : 0.039 0.164 1619 Planarity : 0.004 0.039 1858 Dihedral : 6.400 66.600 1469 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.09 % Allowed : 1.04 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.43 (0.24), residues: 1301 helix: 1.60 (0.22), residues: 569 sheet: 0.67 (0.39), residues: 176 loop : 0.52 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 175 TYR 0.025 0.001 TYR A4528 PHE 0.016 0.001 PHE B 656 TRP 0.007 0.001 TRP B 660 HIS 0.004 0.001 HIS A4558 Details of bonding type rmsd covalent geometry : bond 0.00236 (10675) covalent geometry : angle 0.48629 (14491) hydrogen bonds : bond 0.03487 ( 503) hydrogen bonds : angle 4.64374 ( 1392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 4532 MET cc_start: 0.9529 (mpp) cc_final: 0.9181 (mpp) REVERT: A 4612 LEU cc_start: 0.9775 (tp) cc_final: 0.9553 (tp) REVERT: A 4625 CYS cc_start: 0.9638 (m) cc_final: 0.8918 (m) REVERT: A 4628 PHE cc_start: 0.9623 (m-80) cc_final: 0.9368 (m-80) REVERT: A 4740 MET cc_start: 0.9762 (mtt) cc_final: 0.9462 (mmm) REVERT: A 4767 MET cc_start: 0.9563 (ptp) cc_final: 0.9199 (mmm) REVERT: B 56 MET cc_start: 0.9489 (mtm) cc_final: 0.9060 (mtt) REVERT: B 59 MET cc_start: 0.9450 (ttt) cc_final: 0.8784 (tmm) REVERT: B 69 MET cc_start: 0.9095 (mmm) cc_final: 0.8496 (mmm) REVERT: B 162 MET cc_start: 0.9163 (tpt) cc_final: 0.8771 (mmm) REVERT: B 403 LEU cc_start: 0.9869 (mt) cc_final: 0.9650 (mt) REVERT: B 461 LEU cc_start: 0.9338 (mt) cc_final: 0.9075 (mt) REVERT: B 475 MET cc_start: 0.9758 (mmp) cc_final: 0.9457 (mmm) REVERT: B 844 MET cc_start: 0.8659 (ppp) cc_final: 0.7801 (ppp) REVERT: B 1009 MET cc_start: 0.9217 (mmp) cc_final: 0.8840 (mmm) outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.0797 time to fit residues: 7.4601 Evaluate side-chains 48 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 84 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 56 optimal weight: 0.0980 chunk 25 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 62 optimal weight: 0.0670 chunk 116 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.025319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.018539 restraints weight = 117981.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.019287 restraints weight = 75955.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.019845 restraints weight = 55026.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.020267 restraints weight = 43088.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.020598 restraints weight = 35645.978| |-----------------------------------------------------------------------------| r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10675 Z= 0.089 Angle : 0.477 9.948 14491 Z= 0.247 Chirality : 0.039 0.177 1619 Planarity : 0.004 0.033 1858 Dihedral : 6.220 62.789 1469 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.61 (0.24), residues: 1301 helix: 1.71 (0.23), residues: 564 sheet: 1.06 (0.40), residues: 165 loop : 0.55 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.014 0.001 TYR A4528 PHE 0.017 0.001 PHE B 656 TRP 0.006 0.001 TRP B 416 HIS 0.003 0.001 HIS A4558 Details of bonding type rmsd covalent geometry : bond 0.00185 (10675) covalent geometry : angle 0.47743 (14491) hydrogen bonds : bond 0.03273 ( 503) hydrogen bonds : angle 4.45995 ( 1392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4625 CYS cc_start: 0.9658 (m) cc_final: 0.8933 (m) REVERT: A 4628 PHE cc_start: 0.9609 (m-80) cc_final: 0.9322 (m-80) REVERT: A 4740 MET cc_start: 0.9790 (mtt) cc_final: 0.9471 (mmm) REVERT: A 4767 MET cc_start: 0.9578 (ptp) cc_final: 0.9253 (mmt) REVERT: B 59 MET cc_start: 0.9479 (ttt) cc_final: 0.8817 (tmm) REVERT: B 69 MET cc_start: 0.9264 (mmm) cc_final: 0.8708 (mmm) REVERT: B 162 MET cc_start: 0.9117 (tpt) cc_final: 0.8802 (mmm) REVERT: B 403 LEU cc_start: 0.9889 (mt) cc_final: 0.9682 (mt) REVERT: B 461 LEU cc_start: 0.9353 (mt) cc_final: 0.9079 (mt) REVERT: B 475 MET cc_start: 0.9691 (mmp) cc_final: 0.9440 (mmm) REVERT: B 651 HIS cc_start: 0.9528 (t70) cc_final: 0.9240 (t70) REVERT: B 844 MET cc_start: 0.8640 (ppp) cc_final: 0.7666 (ppp) REVERT: B 904 LEU cc_start: 0.9904 (mm) cc_final: 0.9650 (mm) REVERT: B 1009 MET cc_start: 0.9255 (mmp) cc_final: 0.8876 (mmm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0587 time to fit residues: 5.6353 Evaluate side-chains 48 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 67 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.025334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.018965 restraints weight = 114468.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.019679 restraints weight = 73085.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.020233 restraints weight = 53031.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.020650 restraints weight = 41572.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.020969 restraints weight = 34299.699| |-----------------------------------------------------------------------------| r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10675 Z= 0.099 Angle : 0.476 8.899 14491 Z= 0.246 Chirality : 0.039 0.168 1619 Planarity : 0.004 0.033 1858 Dihedral : 6.137 61.038 1469 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.65 (0.24), residues: 1301 helix: 1.79 (0.22), residues: 564 sheet: 0.95 (0.38), residues: 177 loop : 0.56 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 175 TYR 0.014 0.001 TYR A4528 PHE 0.016 0.001 PHE B 656 TRP 0.006 0.001 TRP B 660 HIS 0.004 0.001 HIS A4558 Details of bonding type rmsd covalent geometry : bond 0.00206 (10675) covalent geometry : angle 0.47603 (14491) hydrogen bonds : bond 0.03212 ( 503) hydrogen bonds : angle 4.34773 ( 1392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4609 MET cc_start: 0.9138 (tpt) cc_final: 0.8879 (tpp) REVERT: A 4625 CYS cc_start: 0.9648 (m) cc_final: 0.8949 (m) REVERT: A 4628 PHE cc_start: 0.9606 (m-80) cc_final: 0.9332 (m-80) REVERT: A 4740 MET cc_start: 0.9770 (mtt) cc_final: 0.9458 (mmm) REVERT: A 4767 MET cc_start: 0.9556 (ptp) cc_final: 0.9242 (mmt) REVERT: B 56 MET cc_start: 0.9473 (mtm) cc_final: 0.8981 (ptp) REVERT: B 59 MET cc_start: 0.9465 (ttt) cc_final: 0.8823 (tmm) REVERT: B 69 MET cc_start: 0.9373 (mmm) cc_final: 0.9037 (mmm) REVERT: B 162 MET cc_start: 0.9126 (tpt) cc_final: 0.8843 (mmm) REVERT: B 403 LEU cc_start: 0.9881 (mt) cc_final: 0.9668 (mt) REVERT: B 461 LEU cc_start: 0.9351 (mt) cc_final: 0.9071 (mt) REVERT: B 475 MET cc_start: 0.9710 (mmp) cc_final: 0.9488 (mmm) REVERT: B 651 HIS cc_start: 0.9554 (t70) cc_final: 0.9266 (t70) REVERT: B 904 LEU cc_start: 0.9920 (mm) cc_final: 0.9603 (mm) REVERT: B 1009 MET cc_start: 0.9261 (mmp) cc_final: 0.8823 (mmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0681 time to fit residues: 6.3576 Evaluate side-chains 46 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 57 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.025376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2369 r_free = 0.2369 target = 0.019016 restraints weight = 114676.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.019730 restraints weight = 73643.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.020270 restraints weight = 53506.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.020683 restraints weight = 42052.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.020985 restraints weight = 34810.943| |-----------------------------------------------------------------------------| r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10675 Z= 0.103 Angle : 0.480 10.324 14491 Z= 0.249 Chirality : 0.039 0.212 1619 Planarity : 0.004 0.032 1858 Dihedral : 6.123 60.275 1469 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.66 (0.24), residues: 1301 helix: 1.82 (0.22), residues: 565 sheet: 0.73 (0.38), residues: 186 loop : 0.63 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 175 TYR 0.013 0.001 TYR A4528 PHE 0.014 0.001 PHE A4598 TRP 0.005 0.001 TRP B 660 HIS 0.004 0.001 HIS A4558 Details of bonding type rmsd covalent geometry : bond 0.00215 (10675) covalent geometry : angle 0.48045 (14491) hydrogen bonds : bond 0.03160 ( 503) hydrogen bonds : angle 4.31434 ( 1392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4625 CYS cc_start: 0.9659 (m) cc_final: 0.8975 (m) REVERT: A 4628 PHE cc_start: 0.9600 (m-80) cc_final: 0.9324 (m-80) REVERT: A 4740 MET cc_start: 0.9762 (mtt) cc_final: 0.9454 (mmm) REVERT: A 4767 MET cc_start: 0.9545 (ptp) cc_final: 0.9240 (mmt) REVERT: B 56 MET cc_start: 0.9475 (mtm) cc_final: 0.8986 (ptp) REVERT: B 59 MET cc_start: 0.9450 (ttt) cc_final: 0.8822 (tmm) REVERT: B 69 MET cc_start: 0.9425 (mmm) cc_final: 0.9126 (mmm) REVERT: B 162 MET cc_start: 0.9100 (tpt) cc_final: 0.8846 (mmm) REVERT: B 403 LEU cc_start: 0.9879 (mt) cc_final: 0.9667 (mt) REVERT: B 461 LEU cc_start: 0.9349 (mt) cc_final: 0.9064 (mt) REVERT: B 651 HIS cc_start: 0.9562 (t70) cc_final: 0.9278 (t70) REVERT: B 844 MET cc_start: 0.7920 (ppp) cc_final: 0.6292 (ppp) REVERT: B 904 LEU cc_start: 0.9928 (mm) cc_final: 0.9672 (mm) REVERT: B 1009 MET cc_start: 0.9275 (mmp) cc_final: 0.8835 (mmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0661 time to fit residues: 6.4323 Evaluate side-chains 46 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 86 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 33 optimal weight: 0.0060 chunk 125 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 0.0970 chunk 100 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.025556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.019165 restraints weight = 114607.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.019900 restraints weight = 73320.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.020456 restraints weight = 53209.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.020881 restraints weight = 41712.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.021190 restraints weight = 34409.217| |-----------------------------------------------------------------------------| r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10675 Z= 0.092 Angle : 0.474 10.132 14491 Z= 0.243 Chirality : 0.039 0.167 1619 Planarity : 0.004 0.032 1858 Dihedral : 6.044 59.141 1469 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.69 (0.24), residues: 1301 helix: 1.84 (0.22), residues: 570 sheet: 0.81 (0.38), residues: 186 loop : 0.61 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.013 0.001 TYR A4528 PHE 0.014 0.001 PHE B 656 TRP 0.005 0.001 TRP B 660 HIS 0.003 0.001 HIS A4558 Details of bonding type rmsd covalent geometry : bond 0.00193 (10675) covalent geometry : angle 0.47390 (14491) hydrogen bonds : bond 0.03099 ( 503) hydrogen bonds : angle 4.24394 ( 1392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4625 CYS cc_start: 0.9655 (m) cc_final: 0.8945 (m) REVERT: A 4628 PHE cc_start: 0.9599 (m-80) cc_final: 0.9325 (m-80) REVERT: A 4740 MET cc_start: 0.9761 (mtt) cc_final: 0.9445 (mmm) REVERT: A 4767 MET cc_start: 0.9566 (ptp) cc_final: 0.9246 (mmt) REVERT: B 56 MET cc_start: 0.9447 (mtm) cc_final: 0.8971 (ptp) REVERT: B 59 MET cc_start: 0.9461 (ttt) cc_final: 0.8860 (tmm) REVERT: B 69 MET cc_start: 0.9460 (mmm) cc_final: 0.9165 (mmm) REVERT: B 403 LEU cc_start: 0.9883 (mt) cc_final: 0.9672 (mt) REVERT: B 461 LEU cc_start: 0.9357 (mt) cc_final: 0.9077 (mt) REVERT: B 475 MET cc_start: 0.9784 (mmp) cc_final: 0.9471 (mmm) REVERT: B 651 HIS cc_start: 0.9556 (t70) cc_final: 0.9276 (t70) REVERT: B 844 MET cc_start: 0.7854 (ppp) cc_final: 0.6143 (ppp) REVERT: B 904 LEU cc_start: 0.9916 (mm) cc_final: 0.9654 (mm) REVERT: B 1009 MET cc_start: 0.9289 (mmp) cc_final: 0.8864 (mmm) REVERT: B 1031 ASP cc_start: 0.8878 (m-30) cc_final: 0.8586 (p0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0747 time to fit residues: 7.2503 Evaluate side-chains 44 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 21 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 43 optimal weight: 0.0870 chunk 12 optimal weight: 0.0770 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.025941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.019468 restraints weight = 113965.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.020210 restraints weight = 73395.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.020783 restraints weight = 53434.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.021225 restraints weight = 41961.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.021547 restraints weight = 34604.700| |-----------------------------------------------------------------------------| r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10675 Z= 0.085 Angle : 0.487 12.123 14491 Z= 0.246 Chirality : 0.039 0.150 1619 Planarity : 0.004 0.032 1858 Dihedral : 5.936 59.069 1469 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.73 (0.24), residues: 1301 helix: 1.85 (0.22), residues: 569 sheet: 0.89 (0.39), residues: 185 loop : 0.64 (0.29), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 175 TYR 0.012 0.001 TYR A4528 PHE 0.015 0.001 PHE B 656 TRP 0.005 0.001 TRP B 416 HIS 0.003 0.000 HIS A4558 Details of bonding type rmsd covalent geometry : bond 0.00179 (10675) covalent geometry : angle 0.48741 (14491) hydrogen bonds : bond 0.03018 ( 503) hydrogen bonds : angle 4.18208 ( 1392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4625 CYS cc_start: 0.9626 (m) cc_final: 0.8889 (m) REVERT: A 4628 PHE cc_start: 0.9598 (m-80) cc_final: 0.9311 (m-80) REVERT: A 4740 MET cc_start: 0.9755 (mtt) cc_final: 0.9430 (mmm) REVERT: A 4767 MET cc_start: 0.9546 (ptp) cc_final: 0.9248 (mmt) REVERT: B 56 MET cc_start: 0.9412 (mtm) cc_final: 0.8971 (ptp) REVERT: B 59 MET cc_start: 0.9453 (ttt) cc_final: 0.9104 (tmm) REVERT: B 69 MET cc_start: 0.9483 (mmm) cc_final: 0.9190 (mmm) REVERT: B 403 LEU cc_start: 0.9890 (mt) cc_final: 0.9671 (mt) REVERT: B 461 LEU cc_start: 0.9355 (mt) cc_final: 0.9057 (mt) REVERT: B 475 MET cc_start: 0.9767 (mmp) cc_final: 0.9359 (mmm) REVERT: B 643 ASP cc_start: 0.9658 (m-30) cc_final: 0.9448 (m-30) REVERT: B 651 HIS cc_start: 0.9536 (t70) cc_final: 0.9257 (t70) REVERT: B 844 MET cc_start: 0.7808 (ppp) cc_final: 0.6074 (ppp) REVERT: B 904 LEU cc_start: 0.9913 (mm) cc_final: 0.9640 (mm) REVERT: B 1009 MET cc_start: 0.9281 (mmp) cc_final: 0.8917 (mmm) REVERT: B 1031 ASP cc_start: 0.8881 (m-30) cc_final: 0.8606 (p0) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0726 time to fit residues: 6.7765 Evaluate side-chains 46 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.025505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.019114 restraints weight = 114091.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.019845 restraints weight = 73504.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.020389 restraints weight = 53536.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.020799 restraints weight = 42104.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.021120 restraints weight = 34855.793| |-----------------------------------------------------------------------------| r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10675 Z= 0.097 Angle : 0.475 11.882 14491 Z= 0.243 Chirality : 0.038 0.150 1619 Planarity : 0.004 0.032 1858 Dihedral : 5.904 59.130 1469 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.81 (0.24), residues: 1301 helix: 1.91 (0.22), residues: 568 sheet: 0.90 (0.39), residues: 185 loop : 0.70 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 48 TYR 0.012 0.001 TYR A4528 PHE 0.014 0.001 PHE B 656 TRP 0.004 0.001 TRP A4738 HIS 0.004 0.001 HIS A4558 Details of bonding type rmsd covalent geometry : bond 0.00204 (10675) covalent geometry : angle 0.47535 (14491) hydrogen bonds : bond 0.02997 ( 503) hydrogen bonds : angle 4.15118 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1381.50 seconds wall clock time: 24 minutes 53.89 seconds (1493.89 seconds total)