Starting phenix.real_space_refine on Wed May 14 01:10:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gh6_40033/05_2025/8gh6_40033.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh6_40033/05_2025/8gh6_40033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gh6_40033/05_2025/8gh6_40033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh6_40033/05_2025/8gh6_40033.map" model { file = "/net/cci-nas-00/data/ceres_data/8gh6_40033/05_2025/8gh6_40033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh6_40033/05_2025/8gh6_40033.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 121 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 178 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 6167 2.51 5 N 2043 2.21 5 O 2357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10785 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7099 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 43, 'TRANS': 854} Chain breaks: 2 Chain: "B" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 952 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "P" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 493 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 831 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 18, 'rna3p_pyr': 14} Link IDs: {'rna2p': 7, 'rna3p': 31} Chain breaks: 2 Chain: "T" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1378 Classifications: {'DNA': 67} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 66} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' MG': 1, ' ZN': 2, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31 SG CYS A 114 33.451 59.687 66.101 1.00 60.08 S ATOM 57 SG CYS A 117 31.222 62.771 66.997 1.00 68.26 S ATOM 5726 SG CYS A 934 15.398 126.086 52.184 1.00 48.69 S ATOM 5752 SG CYS A 938 15.091 129.108 49.930 1.00 52.23 S ATOM 5857 SG CYS A 951 18.013 129.038 52.332 1.00 47.75 S Time building chain proxies: 6.86, per 1000 atoms: 0.64 Number of scatterers: 10785 At special positions: 0 Unit cell: (110.5, 164.424, 107.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 37 16.00 P 178 15.00 Mg 1 11.99 O 2357 8.00 N 2043 7.00 C 6167 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: 2.54 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 130 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 135 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 117 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 114 " pdb=" ZN A1202 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A 946 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 938 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 934 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 951 " Number of angles added : 5 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1654 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 59.7% alpha, 10.7% beta 74 base pairs and 133 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.518A pdb=" N HIS A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 153 through 171 removed outlier: 3.524A pdb=" N LEU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.826A pdb=" N GLY A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 198 Processing helix chain 'A' and resid 199 through 214 removed outlier: 3.852A pdb=" N GLN A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 removed outlier: 3.579A pdb=" N GLU A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.834A pdb=" N TYR A 350 " --> pdb=" O GLU A 346 " (cutoff:3.500A) Proline residue: A 353 - end of helix removed outlier: 3.539A pdb=" N ARG A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 373 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 421 through 436 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 469 through 487 Processing helix chain 'A' and resid 500 through 520 removed outlier: 3.585A pdb=" N ARG A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 removed outlier: 3.824A pdb=" N THR A 536 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 537 " --> pdb=" O PHE A 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 533 through 537' Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 552 through 565 Processing helix chain 'A' and resid 592 through 607 removed outlier: 3.613A pdb=" N VAL A 599 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 604 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 655 removed outlier: 3.513A pdb=" N MET A 654 " --> pdb=" O VAL A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 730 Processing helix chain 'A' and resid 733 through 744 Processing helix chain 'A' and resid 745 through 748 Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'A' and resid 759 through 778 Processing helix chain 'A' and resid 785 through 791 removed outlier: 4.140A pdb=" N TYR A 789 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 816 Proline residue: A 808 - end of helix Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 823 through 831 removed outlier: 3.613A pdb=" N LYS A 831 " --> pdb=" O ARG A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 849 Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 875 through 882 removed outlier: 4.617A pdb=" N GLU A 880 " --> pdb=" O GLU A 877 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A 882 " --> pdb=" O ARG A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 887 Processing helix chain 'A' and resid 888 through 893 removed outlier: 4.422A pdb=" N ARG A 892 " --> pdb=" O THR A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 898 Processing helix chain 'A' and resid 899 through 911 removed outlier: 3.581A pdb=" N ILE A 911 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 932 Processing helix chain 'A' and resid 943 through 950 Processing helix chain 'A' and resid 951 through 953 No H-bonds generated for 'chain 'A' and resid 951 through 953' Processing helix chain 'A' and resid 954 through 976 Processing helix chain 'A' and resid 1018 through 1032 removed outlier: 3.960A pdb=" N LYS A1029 " --> pdb=" O GLU A1025 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR A1030 " --> pdb=" O LYS A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1048 through 1050 No H-bonds generated for 'chain 'A' and resid 1048 through 1050' Processing helix chain 'A' and resid 1066 through 1076 Processing helix chain 'A' and resid 1080 through 1085 Processing helix chain 'A' and resid 1086 through 1105 Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113 removed outlier: 3.770A pdb=" N TRP A 112 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 462 through 467 removed outlier: 6.888A pdb=" N CYS A 445 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA A 571 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR A 447 " --> pdb=" O ALA A 571 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 462 through 467 removed outlier: 6.888A pdb=" N CYS A 445 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA A 571 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR A 447 " --> pdb=" O ALA A 571 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 623 through 626 Processing sheet with id=AA5, first strand: chain 'A' and resid 530 through 531 removed outlier: 4.681A pdb=" N ARG A 657 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 614 through 616 Processing sheet with id=AA7, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AA9, first strand: chain 'A' and resid 851 through 852 Processing sheet with id=AB1, first strand: chain 'A' and resid 981 through 982 removed outlier: 6.738A pdb=" N GLY A1005 " --> pdb=" O ARG A1053 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR A1055 " --> pdb=" O GLY A1005 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE A1007 " --> pdb=" O THR A1055 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N CYS A1057 " --> pdb=" O ILE A1007 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP A1009 " --> pdb=" O CYS A1057 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE A1059 " --> pdb=" O ASP A1009 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLN A1011 " --> pdb=" O ILE A1059 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 986 through 988 removed outlier: 3.551A pdb=" N THR A 988 " --> pdb=" O GLY A 991 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 186 hydrogen bonds 372 hydrogen bond angles 0 basepair planarities 74 basepair parallelities 133 stacking parallelities Total time for adding SS restraints: 6.34 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2686 1.34 - 1.46: 3430 1.46 - 1.58: 4844 1.58 - 1.70: 353 1.70 - 1.83: 53 Bond restraints: 11366 Sorted by residual: bond pdb=" C3' DG B 30 " pdb=" O3' DG B 30 " ideal model delta sigma weight residual 1.422 1.509 -0.087 3.00e-02 1.11e+03 8.36e+00 bond pdb=" C ILE A 470 " pdb=" N PRO A 471 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.28e-02 6.10e+03 7.92e+00 bond pdb=" C VAL A1087 " pdb=" N PRO A1088 " ideal model delta sigma weight residual 1.335 1.371 -0.035 1.36e-02 5.41e+03 6.73e+00 bond pdb=" CB PRO A 439 " pdb=" CG PRO A 439 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.24e+00 bond pdb=" CB GLU A1038 " pdb=" CG GLU A1038 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.54e+00 ... (remaining 11361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.88: 15953 3.88 - 7.76: 164 7.76 - 11.64: 20 11.64 - 15.52: 2 15.52 - 19.39: 1 Bond angle restraints: 16140 Sorted by residual: angle pdb=" CB MET A 640 " pdb=" CG MET A 640 " pdb=" SD MET A 640 " ideal model delta sigma weight residual 112.70 132.09 -19.39 3.00e+00 1.11e-01 4.18e+01 angle pdb=" CA ARG A 171 " pdb=" CB ARG A 171 " pdb=" CG ARG A 171 " ideal model delta sigma weight residual 114.10 126.21 -12.11 2.00e+00 2.50e-01 3.66e+01 angle pdb=" CA GLU A1050 " pdb=" CB GLU A1050 " pdb=" CG GLU A1050 " ideal model delta sigma weight residual 114.10 125.80 -11.70 2.00e+00 2.50e-01 3.42e+01 angle pdb=" CA PRO A 439 " pdb=" N PRO A 439 " pdb=" CD PRO A 439 " ideal model delta sigma weight residual 112.00 104.15 7.85 1.40e+00 5.10e-01 3.15e+01 angle pdb=" C3' A R 245 " pdb=" O3' A R 245 " pdb=" P A R 246 " ideal model delta sigma weight residual 120.20 128.13 -7.93 1.50e+00 4.44e-01 2.79e+01 ... (remaining 16135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.75: 5708 33.75 - 67.50: 770 67.50 - 101.25: 30 101.25 - 135.00: 0 135.00 - 168.75: 5 Dihedral angle restraints: 6513 sinusoidal: 3949 harmonic: 2564 Sorted by residual: dihedral pdb=" C2 TTP A1204 " pdb=" C1' TTP A1204 " pdb=" N1 TTP A1204 " pdb=" O4' TTP A1204 " ideal model delta sinusoidal sigma weight residual 301.68 150.70 150.98 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O4' A R 245 " pdb=" C1' A R 245 " pdb=" N9 A R 245 " pdb=" C4 A R 245 " ideal model delta sinusoidal sigma weight residual 254.00 175.06 78.94 1 1.70e+01 3.46e-03 2.68e+01 dihedral pdb=" CA PRO A 609 " pdb=" C PRO A 609 " pdb=" N GLU A 610 " pdb=" CA GLU A 610 " ideal model delta harmonic sigma weight residual -180.00 -155.34 -24.66 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 6510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1561 0.082 - 0.164: 230 0.164 - 0.246: 19 0.246 - 0.327: 2 0.327 - 0.409: 3 Chirality restraints: 1815 Sorted by residual: chirality pdb=" CB ILE A 911 " pdb=" CA ILE A 911 " pdb=" CG1 ILE A 911 " pdb=" CG2 ILE A 911 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" P DT P 24 " pdb=" OP1 DT P 24 " pdb=" OP2 DT P 24 " pdb=" O5' DT P 24 " both_signs ideal model delta sigma weight residual True 2.35 -2.74 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" C3' A R 245 " pdb=" C4' A R 245 " pdb=" O3' A R 245 " pdb=" C2' A R 245 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 1812 not shown) Planarity restraints: 1449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 438 " 0.079 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 439 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 439 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 439 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1023 " 0.017 2.00e-02 2.50e+03 3.67e-02 2.02e+01 pdb=" CG HIS A1023 " -0.072 2.00e-02 2.50e+03 pdb=" ND1 HIS A1023 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS A1023 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS A1023 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 HIS A1023 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 197 " -0.308 9.50e-02 1.11e+02 1.39e-01 1.45e+01 pdb=" NE ARG A 197 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 197 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG A 197 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 197 " -0.002 2.00e-02 2.50e+03 ... (remaining 1446 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 305 2.68 - 3.24: 8573 3.24 - 3.79: 18741 3.79 - 4.35: 24915 4.35 - 4.90: 36675 Nonbonded interactions: 89209 Sorted by model distance: nonbonded pdb=" O PHE A 530 " pdb="MG MG A1203 " model vdw 2.128 2.170 nonbonded pdb=" OD2 ASP A 628 " pdb="MG MG A1203 " model vdw 2.159 2.170 nonbonded pdb="MG MG A1203 " pdb=" O1A TTP A1204 " model vdw 2.213 2.170 nonbonded pdb=" O LYS A 131 " pdb=" OG1 THR A 139 " model vdw 2.332 3.040 nonbonded pdb=" O ILE A 497 " pdb=" O2' A R 250 " model vdw 2.346 3.040 ... (remaining 89204 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 34.990 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.006 0.114 11374 Z= 0.278 Angle : 1.103 19.394 16145 Z= 0.600 Chirality : 0.058 0.409 1815 Planarity : 0.010 0.139 1449 Dihedral : 23.181 168.754 4859 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.02 % Favored : 97.87 % Rotamer: Outliers : 0.13 % Allowed : 11.42 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.25), residues: 892 helix: -0.88 (0.20), residues: 461 sheet: -0.10 (0.59), residues: 81 loop : -0.31 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A1061 HIS 0.052 0.004 HIS A1023 PHE 0.047 0.004 PHE A 180 TYR 0.054 0.004 TYR A 202 ARG 0.029 0.002 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.15751 ( 567) hydrogen bonds : angle 5.86773 ( 1449) metal coordination : bond 0.01730 ( 8) metal coordination : angle 4.32565 ( 5) covalent geometry : bond 0.00576 (11366) covalent geometry : angle 1.10086 (16140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.883 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.3875 time to fit residues: 51.5179 Evaluate side-chains 76 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.0470 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN A 678 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.180871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134996 restraints weight = 14439.345| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.31 r_work: 0.3392 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11374 Z= 0.141 Angle : 0.605 8.951 16145 Z= 0.343 Chirality : 0.039 0.266 1815 Planarity : 0.005 0.057 1449 Dihedral : 25.543 165.095 3117 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.13 % Favored : 97.76 % Rotamer: Outliers : 2.39 % Allowed : 8.37 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.28), residues: 892 helix: 0.87 (0.23), residues: 473 sheet: 0.43 (0.58), residues: 77 loop : -0.07 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1061 HIS 0.010 0.001 HIS A1096 PHE 0.010 0.001 PHE A 749 TYR 0.014 0.002 TYR A 202 ARG 0.008 0.001 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 567) hydrogen bonds : angle 3.72092 ( 1449) metal coordination : bond 0.01551 ( 8) metal coordination : angle 2.87758 ( 5) covalent geometry : bond 0.00300 (11366) covalent geometry : angle 0.60315 (16140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.936 Fit side-chains REVERT: A 171 ARG cc_start: 0.6700 (ttm-80) cc_final: 0.6055 (tpt90) REVERT: A 976 ASN cc_start: 0.6459 (m-40) cc_final: 0.6166 (t0) outliers start: 18 outliers final: 8 residues processed: 99 average time/residue: 0.3223 time to fit residues: 42.1610 Evaluate side-chains 79 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1055 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 55 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 910 HIS A1096 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.174928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.128744 restraints weight = 14553.676| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.47 r_work: 0.3278 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11374 Z= 0.215 Angle : 0.673 9.357 16145 Z= 0.374 Chirality : 0.043 0.280 1815 Planarity : 0.006 0.048 1449 Dihedral : 25.956 167.037 3117 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.69 % Favored : 97.20 % Rotamer: Outliers : 2.52 % Allowed : 11.02 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.28), residues: 892 helix: 0.96 (0.23), residues: 480 sheet: 0.63 (0.63), residues: 63 loop : -0.22 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1061 HIS 0.010 0.002 HIS A1096 PHE 0.018 0.002 PHE A 749 TYR 0.019 0.002 TYR A 788 ARG 0.005 0.001 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.05437 ( 567) hydrogen bonds : angle 3.79586 ( 1449) metal coordination : bond 0.01342 ( 8) metal coordination : angle 3.18694 ( 5) covalent geometry : bond 0.00491 (11366) covalent geometry : angle 0.67094 (16140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.6984 (ttm-80) cc_final: 0.6252 (tpt90) REVERT: A 1020 ASP cc_start: 0.7601 (m-30) cc_final: 0.7393 (m-30) REVERT: A 1038 GLU cc_start: 0.5750 (mm-30) cc_final: 0.5481 (mt-10) outliers start: 19 outliers final: 11 residues processed: 87 average time/residue: 0.2884 time to fit residues: 33.9495 Evaluate side-chains 78 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1004 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN A 870 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.172427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125407 restraints weight = 14356.828| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.41 r_work: 0.3242 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 11374 Z= 0.296 Angle : 0.739 9.772 16145 Z= 0.407 Chirality : 0.046 0.281 1815 Planarity : 0.006 0.049 1449 Dihedral : 26.285 166.139 3117 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.69 % Favored : 97.20 % Rotamer: Outliers : 2.92 % Allowed : 12.08 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.28), residues: 892 helix: 0.67 (0.23), residues: 478 sheet: 0.21 (0.62), residues: 65 loop : -0.53 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1061 HIS 0.013 0.002 HIS A1096 PHE 0.019 0.002 PHE A 749 TYR 0.022 0.003 TYR A 788 ARG 0.005 0.001 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.06223 ( 567) hydrogen bonds : angle 3.99215 ( 1449) metal coordination : bond 0.01742 ( 8) metal coordination : angle 4.11915 ( 5) covalent geometry : bond 0.00692 (11366) covalent geometry : angle 0.73538 (16140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.891 Fit side-chains REVERT: A 171 ARG cc_start: 0.6877 (ttm-80) cc_final: 0.6263 (tpt90) REVERT: A 617 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: A 687 ILE cc_start: 0.8896 (mt) cc_final: 0.8685 (mt) REVERT: A 1038 GLU cc_start: 0.5723 (mm-30) cc_final: 0.5354 (mt-10) REVERT: A 1046 LEU cc_start: 0.5447 (OUTLIER) cc_final: 0.4988 (pp) outliers start: 22 outliers final: 16 residues processed: 85 average time/residue: 0.3064 time to fit residues: 34.8054 Evaluate side-chains 81 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 974 GLU Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 65 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.176504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.130304 restraints weight = 14376.009| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.38 r_work: 0.3312 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11374 Z= 0.145 Angle : 0.590 9.886 16145 Z= 0.333 Chirality : 0.039 0.269 1815 Planarity : 0.005 0.044 1449 Dihedral : 25.980 167.421 3117 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.68 % Favored : 98.21 % Rotamer: Outliers : 1.86 % Allowed : 13.68 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.29), residues: 892 helix: 1.38 (0.24), residues: 474 sheet: 0.35 (0.63), residues: 65 loop : -0.30 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1061 HIS 0.005 0.001 HIS A1096 PHE 0.011 0.001 PHE A 968 TYR 0.011 0.001 TYR A 788 ARG 0.006 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 567) hydrogen bonds : angle 3.52281 ( 1449) metal coordination : bond 0.01065 ( 8) metal coordination : angle 2.35867 ( 5) covalent geometry : bond 0.00319 (11366) covalent geometry : angle 0.58845 (16140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.892 Fit side-chains REVERT: A 171 ARG cc_start: 0.7074 (ttm-80) cc_final: 0.6369 (tpt90) REVERT: A 346 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6860 (mp0) REVERT: A 1038 GLU cc_start: 0.5651 (mm-30) cc_final: 0.5333 (mt-10) REVERT: A 1046 LEU cc_start: 0.5409 (OUTLIER) cc_final: 0.4997 (pp) outliers start: 14 outliers final: 9 residues processed: 87 average time/residue: 0.2809 time to fit residues: 33.0397 Evaluate side-chains 74 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 0.0870 chunk 28 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN A 744 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.181165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135847 restraints weight = 14609.289| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.41 r_work: 0.3372 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11374 Z= 0.125 Angle : 0.540 10.152 16145 Z= 0.305 Chirality : 0.037 0.246 1815 Planarity : 0.004 0.044 1449 Dihedral : 25.797 170.689 3117 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.68 % Favored : 98.21 % Rotamer: Outliers : 1.99 % Allowed : 14.21 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 892 helix: 1.84 (0.24), residues: 475 sheet: 0.48 (0.63), residues: 65 loop : -0.14 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 701 HIS 0.004 0.001 HIS A1096 PHE 0.008 0.001 PHE A 968 TYR 0.011 0.001 TYR A 202 ARG 0.004 0.000 ARG A 941 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 567) hydrogen bonds : angle 3.29495 ( 1449) metal coordination : bond 0.00896 ( 8) metal coordination : angle 1.79655 ( 5) covalent geometry : bond 0.00266 (11366) covalent geometry : angle 0.53960 (16140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.7056 (ttm-80) cc_final: 0.6335 (tpt90) REVERT: A 190 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6695 (tt) REVERT: A 1038 GLU cc_start: 0.5593 (mm-30) cc_final: 0.5368 (mt-10) REVERT: A 1046 LEU cc_start: 0.5458 (OUTLIER) cc_final: 0.5038 (pp) outliers start: 15 outliers final: 5 residues processed: 95 average time/residue: 0.3491 time to fit residues: 43.0072 Evaluate side-chains 82 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 50 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.176400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130153 restraints weight = 14660.215| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.43 r_work: 0.3301 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11374 Z= 0.180 Angle : 0.605 10.175 16145 Z= 0.336 Chirality : 0.040 0.235 1815 Planarity : 0.005 0.043 1449 Dihedral : 25.893 172.499 3117 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.80 % Favored : 97.09 % Rotamer: Outliers : 2.26 % Allowed : 14.34 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.29), residues: 892 helix: 1.59 (0.24), residues: 476 sheet: 0.46 (0.73), residues: 48 loop : -0.31 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1061 HIS 0.008 0.002 HIS A1096 PHE 0.014 0.001 PHE A 864 TYR 0.017 0.002 TYR A 202 ARG 0.006 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 567) hydrogen bonds : angle 3.47902 ( 1449) metal coordination : bond 0.00976 ( 8) metal coordination : angle 2.19004 ( 5) covalent geometry : bond 0.00410 (11366) covalent geometry : angle 0.60338 (16140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 1.053 Fit side-chains REVERT: A 171 ARG cc_start: 0.7168 (ttm-80) cc_final: 0.6526 (ttp80) REVERT: A 190 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6540 (tt) REVERT: A 617 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6228 (mp0) REVERT: A 1038 GLU cc_start: 0.5608 (mm-30) cc_final: 0.5286 (mt-10) REVERT: A 1046 LEU cc_start: 0.5452 (OUTLIER) cc_final: 0.4992 (pp) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.3301 time to fit residues: 36.4825 Evaluate side-chains 80 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 0.0270 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.177716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.131790 restraints weight = 14466.966| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.39 r_work: 0.3329 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11374 Z= 0.145 Angle : 0.571 10.233 16145 Z= 0.319 Chirality : 0.038 0.226 1815 Planarity : 0.004 0.045 1449 Dihedral : 25.820 173.562 3117 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.91 % Favored : 97.98 % Rotamer: Outliers : 2.26 % Allowed : 13.94 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.29), residues: 892 helix: 1.72 (0.24), residues: 470 sheet: 0.44 (0.61), residues: 65 loop : -0.21 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1061 HIS 0.005 0.001 HIS A1096 PHE 0.010 0.001 PHE A 864 TYR 0.012 0.001 TYR A 202 ARG 0.006 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 567) hydrogen bonds : angle 3.37314 ( 1449) metal coordination : bond 0.00919 ( 8) metal coordination : angle 1.97587 ( 5) covalent geometry : bond 0.00321 (11366) covalent geometry : angle 0.57028 (16140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.7180 (ttm-80) cc_final: 0.6494 (ttp80) REVERT: A 190 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6535 (tt) REVERT: A 347 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7688 (mmt) REVERT: A 515 ASP cc_start: 0.8508 (t70) cc_final: 0.8097 (t70) REVERT: A 617 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6164 (mp0) REVERT: A 1038 GLU cc_start: 0.5692 (mm-30) cc_final: 0.5392 (mt-10) REVERT: A 1046 LEU cc_start: 0.5452 (OUTLIER) cc_final: 0.5014 (pp) outliers start: 17 outliers final: 12 residues processed: 83 average time/residue: 0.3167 time to fit residues: 34.8607 Evaluate side-chains 82 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.179846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134142 restraints weight = 14525.946| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.45 r_work: 0.3350 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11374 Z= 0.129 Angle : 0.548 10.264 16145 Z= 0.307 Chirality : 0.037 0.212 1815 Planarity : 0.004 0.046 1449 Dihedral : 25.696 176.128 3117 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.13 % Favored : 97.76 % Rotamer: Outliers : 2.12 % Allowed : 13.94 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.29), residues: 892 helix: 1.89 (0.24), residues: 475 sheet: 0.51 (0.62), residues: 65 loop : -0.12 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 701 HIS 0.004 0.001 HIS A1096 PHE 0.008 0.001 PHE A 968 TYR 0.019 0.002 TYR A 202 ARG 0.007 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 567) hydrogen bonds : angle 3.26863 ( 1449) metal coordination : bond 0.00832 ( 8) metal coordination : angle 1.70072 ( 5) covalent geometry : bond 0.00281 (11366) covalent geometry : angle 0.54704 (16140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6373 (ttp80) REVERT: A 190 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6497 (tt) REVERT: A 515 ASP cc_start: 0.8340 (t70) cc_final: 0.7916 (t70) REVERT: A 617 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.5942 (mp0) REVERT: A 1038 GLU cc_start: 0.5612 (mm-30) cc_final: 0.5357 (mt-10) REVERT: A 1046 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.4949 (pp) outliers start: 16 outliers final: 10 residues processed: 91 average time/residue: 0.3346 time to fit residues: 39.9694 Evaluate side-chains 83 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 92 optimal weight: 10.0000 chunk 78 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 overall best weight: 1.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.177622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130982 restraints weight = 14433.192| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.35 r_work: 0.3327 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11374 Z= 0.154 Angle : 0.575 9.848 16145 Z= 0.320 Chirality : 0.038 0.204 1815 Planarity : 0.005 0.044 1449 Dihedral : 25.726 176.913 3117 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.35 % Favored : 97.53 % Rotamer: Outliers : 2.12 % Allowed : 14.08 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.29), residues: 892 helix: 1.74 (0.24), residues: 477 sheet: 0.50 (0.62), residues: 65 loop : -0.25 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1061 HIS 0.006 0.001 HIS A1096 PHE 0.012 0.001 PHE A 864 TYR 0.013 0.001 TYR A 788 ARG 0.005 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 567) hydrogen bonds : angle 3.36915 ( 1449) metal coordination : bond 0.00860 ( 8) metal coordination : angle 1.98133 ( 5) covalent geometry : bond 0.00346 (11366) covalent geometry : angle 0.57404 (16140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.7145 (ttm-80) cc_final: 0.6446 (ttp80) REVERT: A 190 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6573 (tt) REVERT: A 515 ASP cc_start: 0.8481 (t70) cc_final: 0.8119 (t70) REVERT: A 551 MET cc_start: 0.6471 (mmp) cc_final: 0.6227 (mmt) REVERT: A 617 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6124 (mp0) REVERT: A 765 MET cc_start: 0.7892 (mmp) cc_final: 0.7260 (mtp) REVERT: A 1038 GLU cc_start: 0.5718 (mm-30) cc_final: 0.5395 (mt-10) REVERT: A 1046 LEU cc_start: 0.5488 (OUTLIER) cc_final: 0.5030 (pp) outliers start: 16 outliers final: 13 residues processed: 81 average time/residue: 0.3251 time to fit residues: 34.3987 Evaluate side-chains 83 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 94 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 102 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.180452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.134571 restraints weight = 14474.114| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.34 r_work: 0.3377 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11374 Z= 0.126 Angle : 0.534 7.757 16145 Z= 0.301 Chirality : 0.037 0.178 1815 Planarity : 0.004 0.046 1449 Dihedral : 25.588 177.969 3117 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.24 % Favored : 97.65 % Rotamer: Outliers : 1.86 % Allowed : 14.21 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 892 helix: 1.95 (0.24), residues: 475 sheet: 0.50 (0.62), residues: 65 loop : -0.09 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1061 HIS 0.004 0.001 HIS A1096 PHE 0.008 0.001 PHE A 968 TYR 0.013 0.001 TYR A 350 ARG 0.006 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 567) hydrogen bonds : angle 3.25176 ( 1449) metal coordination : bond 0.00885 ( 8) metal coordination : angle 1.45028 ( 5) covalent geometry : bond 0.00271 (11366) covalent geometry : angle 0.53395 (16140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6664.65 seconds wall clock time: 115 minutes 14.13 seconds (6914.13 seconds total)