Starting phenix.real_space_refine on Wed Feb 4 14:06:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qgg_53130/02_2026/9qgg_53130_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qgg_53130/02_2026/9qgg_53130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qgg_53130/02_2026/9qgg_53130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qgg_53130/02_2026/9qgg_53130.map" model { file = "/net/cci-nas-00/data/ceres_data/9qgg_53130/02_2026/9qgg_53130_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qgg_53130/02_2026/9qgg_53130_neut.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 1 5.49 5 S 50 5.16 5 C 6817 2.51 5 N 1835 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 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: 10729 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2423 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 275} Chain: "B" Number of atoms: 7661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7661 Classifications: {'peptide': 976} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 48, 'TRANS': 925} Chain breaks: 1 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "E" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.50, per 1000 atoms: 0.23 Number of scatterers: 10729 At special positions: 0 Unit cell: (87.15, 98.77, 128.65, 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 1 15.00 O 2026 8.00 N 1835 7.00 C 6817 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 529.5 milliseconds 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 49.1% alpha, 13.7% 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 4582 through 4592 Processing helix chain 'A' and resid 4618 through 4626 Processing helix chain 'A' and resid 4630 through 4648 removed outlier: 4.173A pdb=" N VAL A4634 " --> pdb=" O HIS A4630 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS A4635 " --> pdb=" O PRO A4631 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR A4646 " --> pdb=" O VAL A4642 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A4648 " --> pdb=" O LEU A4644 " (cutoff:3.500A) Processing helix chain 'A' and resid 4726 through 4730 Processing helix chain 'A' and resid 4746 through 4758 Processing helix chain 'A' and resid 4762 through 4767 removed outlier: 3.691A pdb=" N GLU A4767 " --> pdb=" O TYR A4764 " (cutoff:3.500A) Processing helix chain 'A' and resid 4769 through 4774 removed outlier: 3.750A pdb=" N ARG A4772 " --> pdb=" O GLY A4769 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A4774 " --> pdb=" O GLU A4771 " (cutoff:3.500A) Processing helix chain 'A' and resid 4776 through 4798 removed outlier: 3.620A pdb=" N GLN A4792 " --> pdb=" O SER A4788 " (cutoff:3.500A) Processing helix chain 'A' and resid 4799 through 4805 Processing helix chain 'A' and resid 4810 through 4821 Processing helix chain 'A' and resid 4821 through 4837 Processing helix chain 'A' and resid 4842 through 4869 removed outlier: 3.739A pdb=" N THR A4848 " --> pdb=" O ARG A4844 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A4862 " --> pdb=" O ARG A4858 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A4869 " --> pdb=" O GLU A4865 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 removed outlier: 6.995A pdb=" N ARG B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLN B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 226 through 240 Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.661A pdb=" N SER B 258 " --> pdb=" O HIS B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 271 through 282 removed outlier: 4.300A pdb=" N ALA B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLN B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 313 through 327 Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 450 through 457 removed outlier: 3.834A pdb=" N GLU B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 488 removed outlier: 3.698A pdb=" N THR B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N CYS B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 512 Processing helix chain 'B' and resid 517 through 528 removed outlier: 3.534A pdb=" N ILE B 527 " --> pdb=" O GLN B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 553 removed outlier: 3.558A pdb=" N ASP B 536 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 570 Processing helix chain 'B' and resid 577 through 581 removed outlier: 3.657A pdb=" N GLN B 581 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 595 removed outlier: 3.891A pdb=" N ILE B 593 " --> pdb=" O SER B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 604 Processing helix chain 'B' and resid 613 through 627 Processing helix chain 'B' and resid 644 through 650 removed outlier: 3.643A pdb=" N ASN B 649 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 650 " --> pdb=" O ASN B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 removed outlier: 3.718A pdb=" N VAL B 659 " --> pdb=" O PRO B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 675 removed outlier: 3.536A pdb=" N MET B 674 " --> pdb=" O ALA B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 692 removed outlier: 3.816A pdb=" N GLU B 692 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 702 removed outlier: 3.698A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 727 removed outlier: 3.632A pdb=" N ARG B 716 " --> pdb=" O ASN B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.837A pdb=" N SER B 756 " --> pdb=" O TYR B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 771 Processing helix chain 'B' and resid 775 through 792 Processing helix chain 'B' and resid 792 through 804 removed outlier: 4.850A pdb=" N ASN B 797 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ALA B 798 " --> pdb=" O SER B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 812 Processing helix chain 'B' and resid 817 through 831 removed outlier: 3.842A pdb=" N SER B 825 " --> pdb=" O GLU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 854 Processing helix chain 'B' and resid 854 through 864 Processing helix chain 'B' and resid 893 through 912 Processing helix chain 'B' and resid 918 through 927 removed outlier: 3.588A pdb=" N GLN B 927 " --> pdb=" O ALA B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 976 Processing helix chain 'B' and resid 996 through 1012 Processing helix chain 'B' and resid 1018 through 1027 Processing helix chain 'B' and resid 1033 through 1054 removed outlier: 3.546A pdb=" N THR B1037 " --> pdb=" O ILE B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1116 Processing helix chain 'B' and resid 1136 through 1144 Processing helix chain 'B' and resid 1147 through 1157 Processing helix chain 'E' and resid 22 through 34 Processing helix chain 'E' and resid 37 through 41 Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.893A pdb=" N TYR E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4596 through 4599 removed outlier: 6.686A pdb=" N ILE A4667 " --> pdb=" O ASP A4661 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4602 through 4604 Processing sheet with id=AA3, first strand: chain 'B' and resid 288 through 292 removed outlier: 6.713A pdb=" N ILE B 220 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N HIS B 247 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU B 222 " --> pdb=" O HIS B 247 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP B 219 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL B 308 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 221 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR B 563 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 351 through 353 Processing sheet with id=AA5, first strand: chain 'B' and resid 410 through 411 removed outlier: 4.603A pdb=" N TYR B 392 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL B 398 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY B 434 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY B 435 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR B 378 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE B 369 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 376 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 680 through 683 removed outlier: 6.296A pdb=" N ILE B 635 " --> pdb=" O THR B 681 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N TYR B 683 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 637 " --> pdb=" O TYR B 683 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LYS B 606 " --> pdb=" O GLY B 705 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ALA B 707 " --> pdb=" O LYS B 606 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE B 608 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 733 " --> pdb=" O ASN B 708 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1084 through 1086 Processing sheet with id=AA8, first strand: chain 'B' and resid 1096 through 1099 removed outlier: 6.287A pdb=" N PHE B1097 " --> pdb=" O ARG B1187 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR B1189 " --> pdb=" O PHE B1097 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL B1099 " --> pdb=" O THR B1189 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL B1168 " --> pdb=" O GLN B1125 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLN B1125 " --> pdb=" O VAL B1168 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU B1170 " --> pdb=" O LEU B1123 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU B1123 " --> pdb=" O GLU B1170 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS B1172 " --> pdb=" O THR B1121 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN B1125 " --> pdb=" O MET B1129 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N MET B1129 " --> pdb=" O GLN B1125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1096 through 1099 removed outlier: 6.287A pdb=" N PHE B1097 " --> pdb=" O ARG B1187 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR B1189 " --> pdb=" O PHE B1097 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL B1099 " --> pdb=" O THR B1189 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS B1173 " --> pdb=" O VAL B1181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 12 through 16 removed outlier: 8.920A pdb=" N LEU E 67 " --> pdb=" O GLN E 2 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE E 4 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU E 69 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS E 6 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG E 42 " --> pdb=" O VAL E 70 " (cutoff:3.500A) 517 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3465 1.34 - 1.46: 1822 1.46 - 1.58: 5602 1.58 - 1.70: 1 1.70 - 1.82: 74 Bond restraints: 10964 Sorted by residual: bond pdb=" CB CYS B 767 " pdb=" SG CYS B 767 " ideal model delta sigma weight residual 1.808 1.420 0.388 3.30e-02 9.18e+02 1.39e+02 bond pdb=" CA SER E 20 " pdb=" CB SER E 20 " ideal model delta sigma weight residual 1.533 1.476 0.058 1.63e-02 3.76e+03 1.25e+01 bond pdb=" CB THR B1036 " pdb=" OG1 THR B1036 " ideal model delta sigma weight residual 1.433 1.394 0.039 1.60e-02 3.91e+03 6.03e+00 bond pdb=" CA THR E 22 " pdb=" C THR E 22 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.31e-02 5.83e+03 5.73e+00 bond pdb=" CZ ARG C 74 " pdb=" NH2 ARG C 74 " ideal model delta sigma weight residual 1.330 1.299 0.031 1.30e-02 5.92e+03 5.65e+00 ... (remaining 10959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 14472 1.85 - 3.70: 308 3.70 - 5.55: 54 5.55 - 7.39: 6 7.39 - 9.24: 4 Bond angle restraints: 14844 Sorted by residual: angle pdb=" CA PHE B 555 " pdb=" CB PHE B 555 " pdb=" CG PHE B 555 " ideal model delta sigma weight residual 113.80 118.14 -4.34 1.00e+00 1.00e+00 1.88e+01 angle pdb=" OE1 GLN B 356 " pdb=" CD GLN B 356 " pdb=" NE2 GLN B 356 " ideal model delta sigma weight residual 122.60 118.52 4.08 1.00e+00 1.00e+00 1.66e+01 angle pdb=" CA THR E 7 " pdb=" C THR E 7 " pdb=" N LEU E 8 " ideal model delta sigma weight residual 115.27 120.27 -5.00 1.30e+00 5.92e-01 1.48e+01 angle pdb=" OE1 GLN B 545 " pdb=" CD GLN B 545 " pdb=" NE2 GLN B 545 " ideal model delta sigma weight residual 122.60 118.76 3.84 1.00e+00 1.00e+00 1.47e+01 angle pdb=" CB HIS E 68 " pdb=" CG HIS E 68 " pdb=" CD2 HIS E 68 " ideal model delta sigma weight residual 131.20 126.28 4.92 1.30e+00 5.92e-01 1.43e+01 ... (remaining 14839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 5972 17.20 - 34.40: 507 34.40 - 51.60: 109 51.60 - 68.80: 41 68.80 - 86.00: 17 Dihedral angle restraints: 6646 sinusoidal: 2720 harmonic: 3926 Sorted by residual: dihedral pdb=" CA LEU B1070 " pdb=" C LEU B1070 " pdb=" N PRO B1071 " pdb=" CA PRO B1071 " ideal model delta harmonic sigma weight residual 0.00 -26.99 26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA TRP A4732 " pdb=" C TRP A4732 " pdb=" N HIS A4733 " pdb=" CA HIS A4733 " ideal model delta harmonic sigma weight residual 180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ASP E 21 " pdb=" CB ASP E 21 " pdb=" CG ASP E 21 " pdb=" OD1 ASP E 21 " ideal model delta sinusoidal sigma weight residual -30.00 -89.77 59.77 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 6643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1410 0.061 - 0.123: 198 0.123 - 0.184: 26 0.184 - 0.245: 3 0.245 - 0.306: 3 Chirality restraints: 1640 Sorted by residual: chirality pdb=" CA ARG C 74 " pdb=" N ARG C 74 " pdb=" C ARG C 74 " pdb=" CB ARG C 74 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA VAL E 17 " pdb=" N VAL E 17 " pdb=" C VAL E 17 " pdb=" CB VAL E 17 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA LEU B1070 " pdb=" N LEU B1070 " pdb=" C LEU B1070 " pdb=" CB LEU B1070 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1637 not shown) Planarity restraints: 1935 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B1065 " 0.053 2.00e-02 2.50e+03 3.31e-02 1.92e+01 pdb=" CG PHE B1065 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B1065 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B1065 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE B1065 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B1065 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B1065 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 68 " -0.048 2.00e-02 2.50e+03 3.55e-02 1.89e+01 pdb=" CG HIS E 68 " 0.050 2.00e-02 2.50e+03 pdb=" ND1 HIS E 68 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS E 68 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS E 68 " -0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS E 68 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 559 " -0.057 2.00e-02 2.50e+03 2.90e-02 1.68e+01 pdb=" CG TYR B 559 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 559 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 559 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 559 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 559 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 559 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 559 " -0.029 2.00e-02 2.50e+03 ... (remaining 1932 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 2 2.04 - 2.75: 1281 2.75 - 3.47: 14834 3.47 - 4.18: 25709 4.18 - 4.90: 46843 Nonbonded interactions: 88669 Sorted by model distance: nonbonded pdb=" SG CYS B 767 " pdb=" C ALA C 76 " model vdw 1.325 3.630 nonbonded pdb=" SG CYS A4725 " pdb=" CB ALA C 76 " model vdw 1.808 3.820 nonbonded pdb=" SG CYS B 767 " pdb=" O ALA C 76 " model vdw 2.226 3.400 nonbonded pdb=" O LEU B 710 " pdb=" CB ALA E 76 " model vdw 2.284 3.460 nonbonded pdb=" CB CYS B 767 " pdb=" C ALA C 76 " model vdw 2.359 3.670 ... (remaining 88664 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 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: 2.680 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.060 Find NCS groups from input model: 0.030 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:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 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 : 0.005 0.388 10965 Z= 0.219 Angle : 0.619 9.243 14844 Z= 0.359 Chirality : 0.045 0.306 1640 Planarity : 0.004 0.053 1935 Dihedral : 14.747 86.004 4102 Min Nonbonded Distance : 1.325 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.85 % Allowed : 10.27 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.62 (0.23), residues: 1339 helix: 1.67 (0.22), residues: 568 sheet: 1.54 (0.36), residues: 208 loop : 0.39 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1159 TYR 0.057 0.002 TYR B 559 PHE 0.053 0.002 PHE B1065 TRP 0.035 0.001 TRP A4732 HIS 0.003 0.000 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00500 (10964) covalent geometry : angle 0.61947 (14844) hydrogen bonds : bond 0.14604 ( 513) hydrogen bonds : angle 5.57702 ( 1446) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.359 Fit side-chains REVERT: B 366 ILE cc_start: 0.9162 (mt) cc_final: 0.8932 (mp) REVERT: B 391 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: B 806 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7068 (pp30) REVERT: B 874 GLN cc_start: 0.9253 (mp10) cc_final: 0.8820 (pm20) REVERT: B 937 ARG cc_start: 0.7359 (ptm160) cc_final: 0.7051 (ppp80) REVERT: B 965 ARG cc_start: 0.8628 (mtt-85) cc_final: 0.8146 (mtm-85) REVERT: B 1159 ARG cc_start: 0.8930 (mtm110) cc_final: 0.8621 (mtm110) REVERT: C 74 ARG cc_start: 0.5691 (OUTLIER) cc_final: 0.5346 (mpp80) REVERT: E 18 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8753 (mm-30) REVERT: E 21 ASP cc_start: 0.9044 (OUTLIER) cc_final: 0.8242 (m-30) REVERT: E 22 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.6629 (p) REVERT: E 33 LYS cc_start: 0.8840 (mttm) cc_final: 0.8619 (mttp) REVERT: E 34 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8567 (mm-30) REVERT: E 64 GLU cc_start: 0.9245 (mp0) cc_final: 0.8803 (mp0) outliers start: 10 outliers final: 3 residues processed: 75 average time/residue: 0.6520 time to fit residues: 52.2804 Evaluate side-chains 74 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4694 ASP Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 22 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0050 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.046293 restraints weight = 24582.924| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 2.95 r_work: 0.2402 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 10965 Z= 0.276 Angle : 0.548 7.472 14844 Z= 0.282 Chirality : 0.044 0.155 1640 Planarity : 0.004 0.038 1935 Dihedral : 5.445 55.505 1480 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.93 % Allowed : 10.61 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.68 (0.23), residues: 1339 helix: 1.81 (0.22), residues: 573 sheet: 1.12 (0.35), residues: 220 loop : 0.49 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1159 TYR 0.018 0.001 TYR B 901 PHE 0.016 0.001 PHE B1112 TRP 0.019 0.002 TRP A4732 HIS 0.005 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00658 (10964) covalent geometry : angle 0.54768 (14844) hydrogen bonds : bond 0.04789 ( 513) hydrogen bonds : angle 4.66369 ( 1446) Misc. bond : bond 0.00160 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.395 Fit side-chains REVERT: B 366 ILE cc_start: 0.9354 (mt) cc_final: 0.9143 (mp) REVERT: B 806 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7080 (pp30) REVERT: B 874 GLN cc_start: 0.9224 (mp10) cc_final: 0.8761 (pm20) REVERT: B 937 ARG cc_start: 0.7576 (ptm160) cc_final: 0.7265 (ppp80) REVERT: B 965 ARG cc_start: 0.8655 (mtt-85) cc_final: 0.8143 (mtm-85) REVERT: C 74 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.5636 (mtm-85) REVERT: E 18 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8838 (mm-30) REVERT: E 21 ASP cc_start: 0.8900 (m-30) cc_final: 0.8060 (m-30) REVERT: E 64 GLU cc_start: 0.9272 (mp0) cc_final: 0.8801 (mp0) outliers start: 11 outliers final: 4 residues processed: 72 average time/residue: 0.7829 time to fit residues: 60.0704 Evaluate side-chains 68 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 36 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 120 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 741 ASN B1011 ASN E 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.048435 restraints weight = 24740.435| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 3.06 r_work: 0.2425 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 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 : 0.003 0.030 10965 Z= 0.119 Angle : 0.469 7.073 14844 Z= 0.241 Chirality : 0.040 0.141 1640 Planarity : 0.003 0.036 1935 Dihedral : 4.631 40.148 1473 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.78 % Allowed : 10.02 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.77 (0.23), residues: 1339 helix: 1.91 (0.22), residues: 573 sheet: 1.07 (0.35), residues: 220 loop : 0.55 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1159 TYR 0.016 0.001 TYR B 901 PHE 0.015 0.001 PHE B1112 TRP 0.025 0.001 TRP A4732 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00271 (10964) covalent geometry : angle 0.46867 (14844) hydrogen bonds : bond 0.03723 ( 513) hydrogen bonds : angle 4.37651 ( 1446) Misc. bond : bond 0.00068 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.350 Fit side-chains REVERT: B 391 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.7677 (m-30) REVERT: B 418 TYR cc_start: 0.7968 (m-80) cc_final: 0.7690 (m-80) REVERT: B 762 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8806 (mmtt) REVERT: B 806 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7020 (pp30) REVERT: B 874 GLN cc_start: 0.9221 (mp10) cc_final: 0.8731 (pm20) REVERT: B 898 ASP cc_start: 0.8886 (m-30) cc_final: 0.8501 (m-30) REVERT: B 937 ARG cc_start: 0.7547 (ptm160) cc_final: 0.7244 (ppp80) REVERT: B 965 ARG cc_start: 0.8636 (mtt-85) cc_final: 0.8128 (mtm-85) REVERT: C 74 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.5651 (mtm-85) REVERT: E 18 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8681 (mm-30) REVERT: E 21 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: E 64 GLU cc_start: 0.9284 (mp0) cc_final: 0.8862 (mp0) outliers start: 21 outliers final: 4 residues processed: 77 average time/residue: 0.8017 time to fit residues: 65.6861 Evaluate side-chains 72 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4694 ASP Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 36 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 121 optimal weight: 0.0470 chunk 99 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 741 ASN E 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.068051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.049882 restraints weight = 24483.160| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 2.98 r_work: 0.2463 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10965 Z= 0.093 Angle : 0.452 6.856 14844 Z= 0.231 Chirality : 0.040 0.137 1640 Planarity : 0.004 0.066 1935 Dihedral : 4.354 36.806 1473 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.53 % Allowed : 10.53 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.85 (0.23), residues: 1339 helix: 2.01 (0.22), residues: 573 sheet: 1.10 (0.36), residues: 211 loop : 0.56 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1159 TYR 0.014 0.001 TYR B 901 PHE 0.013 0.001 PHE B1108 TRP 0.026 0.001 TRP A4732 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00203 (10964) covalent geometry : angle 0.45207 (14844) hydrogen bonds : bond 0.03244 ( 513) hydrogen bonds : angle 4.19084 ( 1446) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.478 Fit side-chains REVERT: B 391 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.7550 (m-30) REVERT: B 408 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7757 (pp30) REVERT: B 596 LYS cc_start: 0.9000 (tttt) cc_final: 0.8697 (tptt) REVERT: B 762 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8277 (mmmt) REVERT: B 806 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6988 (pp30) REVERT: B 874 GLN cc_start: 0.9206 (mp10) cc_final: 0.8804 (pm20) REVERT: B 898 ASP cc_start: 0.8818 (m-30) cc_final: 0.8465 (m-30) REVERT: B 937 ARG cc_start: 0.7528 (ptm160) cc_final: 0.7220 (ppp80) REVERT: B 965 ARG cc_start: 0.8616 (mtt-85) cc_final: 0.8096 (mtm-85) REVERT: C 74 ARG cc_start: 0.6113 (OUTLIER) cc_final: 0.5770 (mpp-170) REVERT: E 18 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8660 (mm-30) REVERT: E 21 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: E 62 GLN cc_start: 0.8782 (pt0) cc_final: 0.8567 (mt0) REVERT: E 64 GLU cc_start: 0.9303 (mp0) cc_final: 0.8846 (mp0) REVERT: E 74 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7604 (ptm160) outliers start: 18 outliers final: 2 residues processed: 80 average time/residue: 0.7335 time to fit residues: 62.6405 Evaluate side-chains 72 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4694 ASP Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 74 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 70 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 741 ASN E 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.066521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.048275 restraints weight = 24432.390| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 2.98 r_work: 0.2444 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10965 Z= 0.163 Angle : 0.478 6.843 14844 Z= 0.245 Chirality : 0.041 0.151 1640 Planarity : 0.003 0.035 1935 Dihedral : 4.381 37.042 1472 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.19 % Allowed : 10.61 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.82 (0.23), residues: 1339 helix: 2.03 (0.22), residues: 574 sheet: 0.98 (0.35), residues: 211 loop : 0.54 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1159 TYR 0.016 0.001 TYR B 901 PHE 0.014 0.001 PHE B1108 TRP 0.018 0.001 TRP A4732 HIS 0.004 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00385 (10964) covalent geometry : angle 0.47848 (14844) hydrogen bonds : bond 0.03718 ( 513) hydrogen bonds : angle 4.22740 ( 1446) Misc. bond : bond 0.00084 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.457 Fit side-chains REVERT: B 391 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: B 806 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7096 (pp30) REVERT: B 874 GLN cc_start: 0.9192 (mp10) cc_final: 0.8793 (pm20) REVERT: B 898 ASP cc_start: 0.8850 (m-30) cc_final: 0.8496 (m-30) REVERT: B 937 ARG cc_start: 0.7615 (ptm160) cc_final: 0.7317 (ppp80) REVERT: B 965 ARG cc_start: 0.8638 (mtt-85) cc_final: 0.8111 (mtm-85) REVERT: C 74 ARG cc_start: 0.5955 (OUTLIER) cc_final: 0.5678 (mpp-170) REVERT: E 18 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8692 (mm-30) REVERT: E 21 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: E 64 GLU cc_start: 0.9331 (mp0) cc_final: 0.8858 (mp0) REVERT: E 74 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8048 (ptp-110) outliers start: 14 outliers final: 4 residues processed: 71 average time/residue: 0.7160 time to fit residues: 54.1356 Evaluate side-chains 72 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4694 ASP Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 74 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 24 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4639 GLN B 741 ASN E 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.065728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.047470 restraints weight = 24619.019| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 2.96 r_work: 0.2403 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10965 Z= 0.222 Angle : 0.509 7.333 14844 Z= 0.261 Chirality : 0.043 0.147 1640 Planarity : 0.003 0.036 1935 Dihedral : 4.534 37.841 1472 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.10 % Allowed : 11.21 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.75 (0.23), residues: 1339 helix: 1.99 (0.22), residues: 574 sheet: 0.83 (0.35), residues: 223 loop : 0.53 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1159 TYR 0.018 0.001 TYR B 901 PHE 0.015 0.001 PHE B1112 TRP 0.019 0.001 TRP A4732 HIS 0.005 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00530 (10964) covalent geometry : angle 0.50946 (14844) hydrogen bonds : bond 0.04127 ( 513) hydrogen bonds : angle 4.33599 ( 1446) Misc. bond : bond 0.00108 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.345 Fit side-chains REVERT: B 391 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: B 408 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7861 (pp30) REVERT: B 418 TYR cc_start: 0.7928 (m-80) cc_final: 0.7721 (m-80) REVERT: B 806 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7121 (pp30) REVERT: B 874 GLN cc_start: 0.9166 (mp10) cc_final: 0.8728 (pm20) REVERT: B 898 ASP cc_start: 0.8903 (m-30) cc_final: 0.8557 (m-30) REVERT: B 937 ARG cc_start: 0.7636 (ptm160) cc_final: 0.7339 (ppp80) REVERT: B 965 ARG cc_start: 0.8677 (mtt-85) cc_final: 0.8162 (mtm-85) REVERT: C 74 ARG cc_start: 0.6098 (OUTLIER) cc_final: 0.5727 (mpp-170) REVERT: E 18 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8646 (mm-30) REVERT: E 21 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.7691 (m-30) REVERT: E 64 GLU cc_start: 0.9336 (mp0) cc_final: 0.8852 (mp0) REVERT: E 74 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8245 (ptp-110) outliers start: 13 outliers final: 2 residues processed: 72 average time/residue: 0.7010 time to fit residues: 53.7984 Evaluate side-chains 72 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4694 ASP Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 74 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 18 optimal weight: 0.0970 chunk 62 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 741 ASN E 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.067356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.049061 restraints weight = 24300.657| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 2.98 r_work: 0.2449 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10965 Z= 0.107 Angle : 0.464 8.094 14844 Z= 0.237 Chirality : 0.040 0.140 1640 Planarity : 0.003 0.036 1935 Dihedral : 4.225 36.347 1470 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.02 % Allowed : 11.21 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.82 (0.23), residues: 1339 helix: 2.06 (0.22), residues: 574 sheet: 0.83 (0.35), residues: 211 loop : 0.57 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B1159 TYR 0.015 0.001 TYR B 901 PHE 0.013 0.001 PHE B 428 TRP 0.026 0.001 TRP A4732 HIS 0.004 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00245 (10964) covalent geometry : angle 0.46415 (14844) hydrogen bonds : bond 0.03349 ( 513) hydrogen bonds : angle 4.15624 ( 1446) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.444 Fit side-chains REVERT: B 391 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: B 408 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7773 (pp30) REVERT: B 418 TYR cc_start: 0.7897 (m-80) cc_final: 0.7628 (m-80) REVERT: B 806 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7083 (pp30) REVERT: B 874 GLN cc_start: 0.9162 (mp10) cc_final: 0.8804 (pm20) REVERT: B 898 ASP cc_start: 0.8860 (m-30) cc_final: 0.8532 (m-30) REVERT: B 937 ARG cc_start: 0.7602 (ptm160) cc_final: 0.7308 (ppp80) REVERT: B 965 ARG cc_start: 0.8651 (mtt-85) cc_final: 0.8155 (mtm110) REVERT: B 1159 ARG cc_start: 0.8983 (mtm110) cc_final: 0.8542 (mtm110) REVERT: C 74 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.5638 (mpp-170) REVERT: E 18 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8637 (mm-30) REVERT: E 21 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: E 64 GLU cc_start: 0.9318 (mp0) cc_final: 0.8761 (mp0) outliers start: 12 outliers final: 1 residues processed: 72 average time/residue: 0.7800 time to fit residues: 59.8760 Evaluate side-chains 72 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4694 ASP Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain E residue 21 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 122 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 741 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.065459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.047228 restraints weight = 24596.614| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 2.96 r_work: 0.2396 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 10965 Z= 0.251 Angle : 0.529 7.811 14844 Z= 0.270 Chirality : 0.043 0.147 1640 Planarity : 0.004 0.036 1935 Dihedral : 4.402 37.916 1470 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.93 % Allowed : 11.46 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.74 (0.23), residues: 1339 helix: 2.01 (0.22), residues: 575 sheet: 0.77 (0.35), residues: 223 loop : 0.52 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1159 TYR 0.019 0.001 TYR B 901 PHE 0.016 0.001 PHE B1108 TRP 0.028 0.002 TRP A4732 HIS 0.005 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00600 (10964) covalent geometry : angle 0.52876 (14844) hydrogen bonds : bond 0.04200 ( 513) hydrogen bonds : angle 4.33083 ( 1446) Misc. bond : bond 0.00121 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.482 Fit side-chains REVERT: B 391 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.7965 (m-30) REVERT: B 408 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7874 (pp30) REVERT: B 806 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7123 (pp30) REVERT: B 874 GLN cc_start: 0.9146 (mp10) cc_final: 0.8808 (pm20) REVERT: B 898 ASP cc_start: 0.8913 (m-30) cc_final: 0.8567 (m-30) REVERT: B 937 ARG cc_start: 0.7681 (ptm160) cc_final: 0.7385 (ppp80) REVERT: B 965 ARG cc_start: 0.8688 (mtt-85) cc_final: 0.8177 (mtm-85) REVERT: C 74 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.5681 (mpp-170) REVERT: E 18 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8611 (mm-30) REVERT: E 21 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: E 64 GLU cc_start: 0.9321 (mp0) cc_final: 0.8809 (mp0) outliers start: 11 outliers final: 1 residues processed: 72 average time/residue: 0.7814 time to fit residues: 59.8627 Evaluate side-chains 70 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4694 ASP Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain E residue 21 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 127 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 741 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.067280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.049052 restraints weight = 24160.720| |-----------------------------------------------------------------------------| r_work (start): 0.2605 rms_B_bonded: 2.95 r_work: 0.2443 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10965 Z= 0.110 Angle : 0.475 7.909 14844 Z= 0.242 Chirality : 0.040 0.140 1640 Planarity : 0.003 0.040 1935 Dihedral : 4.248 36.516 1470 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.93 % Allowed : 11.88 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.80 (0.23), residues: 1339 helix: 2.06 (0.22), residues: 574 sheet: 0.82 (0.36), residues: 214 loop : 0.54 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B1159 TYR 0.016 0.001 TYR B 901 PHE 0.014 0.001 PHE B 428 TRP 0.032 0.001 TRP A4732 HIS 0.004 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00253 (10964) covalent geometry : angle 0.47529 (14844) hydrogen bonds : bond 0.03383 ( 513) hydrogen bonds : angle 4.15392 ( 1446) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.441 Fit side-chains REVERT: B 391 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.7597 (m-30) REVERT: B 408 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7790 (pp30) REVERT: B 418 TYR cc_start: 0.7849 (m-80) cc_final: 0.7634 (m-80) REVERT: B 806 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7037 (pp30) REVERT: B 874 GLN cc_start: 0.9152 (mp10) cc_final: 0.8661 (pm20) REVERT: B 898 ASP cc_start: 0.8888 (m-30) cc_final: 0.8567 (m-30) REVERT: B 937 ARG cc_start: 0.7659 (ptm160) cc_final: 0.7373 (ppp80) REVERT: B 965 ARG cc_start: 0.8650 (mtt-85) cc_final: 0.8170 (mtm110) REVERT: B 1159 ARG cc_start: 0.8989 (mtm110) cc_final: 0.8554 (mtm110) REVERT: C 74 ARG cc_start: 0.5832 (OUTLIER) cc_final: 0.5588 (mpp-170) REVERT: E 18 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8600 (mm-30) REVERT: E 21 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: E 64 GLU cc_start: 0.9293 (mp0) cc_final: 0.8733 (mp0) outliers start: 11 outliers final: 1 residues processed: 73 average time/residue: 0.7387 time to fit residues: 57.5446 Evaluate side-chains 70 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4694 ASP Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain E residue 21 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 58 optimal weight: 0.0070 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 121 optimal weight: 0.3980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 741 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.067346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.049106 restraints weight = 24295.340| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 2.97 r_work: 0.2451 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10965 Z= 0.116 Angle : 0.475 8.483 14844 Z= 0.240 Chirality : 0.040 0.139 1640 Planarity : 0.003 0.041 1935 Dihedral : 4.147 35.853 1470 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.68 % Allowed : 12.05 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.84 (0.23), residues: 1339 helix: 2.10 (0.22), residues: 575 sheet: 0.85 (0.36), residues: 214 loop : 0.55 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B1159 TYR 0.015 0.001 TYR B 901 PHE 0.015 0.001 PHE B 428 TRP 0.032 0.001 TRP A4732 HIS 0.004 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00270 (10964) covalent geometry : angle 0.47515 (14844) hydrogen bonds : bond 0.03309 ( 513) hydrogen bonds : angle 4.09273 ( 1446) Misc. bond : bond 0.00044 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.436 Fit side-chains REVERT: B 391 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: B 408 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7775 (pp30) REVERT: B 418 TYR cc_start: 0.7845 (m-80) cc_final: 0.7620 (m-80) REVERT: B 796 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8450 (mt-10) REVERT: B 806 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7036 (pp30) REVERT: B 874 GLN cc_start: 0.9138 (mp10) cc_final: 0.8660 (pm20) REVERT: B 898 ASP cc_start: 0.8839 (m-30) cc_final: 0.8507 (m-30) REVERT: B 937 ARG cc_start: 0.7686 (ptm160) cc_final: 0.7395 (ppp80) REVERT: B 965 ARG cc_start: 0.8613 (mtt-85) cc_final: 0.8138 (mtm110) REVERT: B 1159 ARG cc_start: 0.8970 (mtm110) cc_final: 0.8529 (mtm110) REVERT: C 74 ARG cc_start: 0.5828 (OUTLIER) cc_final: 0.5553 (mpp-170) REVERT: E 18 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8610 (mm-30) REVERT: E 21 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.7643 (m-30) REVERT: E 64 GLU cc_start: 0.9264 (mp0) cc_final: 0.8746 (mp0) outliers start: 8 outliers final: 1 residues processed: 71 average time/residue: 0.8290 time to fit residues: 62.7078 Evaluate side-chains 72 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4694 ASP Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain E residue 21 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 741 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.067512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.049249 restraints weight = 24467.791| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 2.98 r_work: 0.2454 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10965 Z= 0.113 Angle : 0.471 7.783 14844 Z= 0.239 Chirality : 0.040 0.140 1640 Planarity : 0.003 0.040 1935 Dihedral : 4.115 35.616 1470 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.59 % Allowed : 11.88 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.86 (0.23), residues: 1339 helix: 2.12 (0.22), residues: 575 sheet: 0.85 (0.36), residues: 214 loop : 0.55 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B1159 TYR 0.015 0.001 TYR B 901 PHE 0.014 0.001 PHE B 428 TRP 0.032 0.001 TRP A4732 HIS 0.004 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00262 (10964) covalent geometry : angle 0.47061 (14844) hydrogen bonds : bond 0.03255 ( 513) hydrogen bonds : angle 4.07224 ( 1446) Misc. bond : bond 0.00061 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2887.96 seconds wall clock time: 50 minutes 10.07 seconds (3010.07 seconds total)