Starting phenix.real_space_refine on Fri Jul 3 03:24:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nl3_49516/07_2026/9nl3_49516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nl3_49516/07_2026/9nl3_49516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nl3_49516/07_2026/9nl3_49516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nl3_49516/07_2026/9nl3_49516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nl3_49516/07_2026/9nl3_49516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nl3_49516/07_2026/9nl3_49516.map" } resolution = 3.2 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= 0.004 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 4 6.06 5 P 159 5.49 5 Mg 1 5.21 5 S 51 5.16 5 C 6993 2.51 5 N 2165 2.21 5 O 2566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11939 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8655 Classifications: {'peptide': 1079} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1028} Chain breaks: 2 Chain: "B" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 791 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "P" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} 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: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1140 Classifications: {'RNA': 53} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 24, 'rna3p_pyr': 17} Link IDs: {'rna2p': 12, 'rna3p': 40} Chain breaks: 2 Chain: "T" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1052 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 34 Unusual residues: {' MG': 1, ' ZN': 4, 'TTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 310 SG CYS A 41 55.775 30.513 64.736 1.00 86.53 S ATOM 330 SG CYS A 44 58.211 31.927 62.111 1.00 93.20 S ATOM 465 SG CYS A 61 54.773 31.941 61.304 1.00 82.06 S ATOM 579 SG CYS A 76 76.412 46.802 52.258 1.00 97.02 S ATOM 601 SG CYS A 79 74.639 44.489 54.904 1.00 89.57 S ATOM 7222 SG CYS A 991 31.997 32.857 97.447 1.00 79.38 S ATOM 7249 SG CYS A 994 28.609 32.222 98.899 1.00 63.53 S ATOM 7348 SG CYS A1008 31.554 33.293 101.124 1.00 79.09 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' TTP A1206 " occ=0.65 ... (27 atoms not shown) pdb=" PG TTP A1206 " occ=0.65 Time building chain proxies: 2.58, per 1000 atoms: 0.22 Number of scatterers: 11939 At special positions: 0 Unit cell: (122.616, 119.472, 139.384, 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 4 29.99 S 51 16.00 P 159 15.00 Mg 1 11.99 O 2566 8.00 N 2165 7.00 C 6993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 11 " - pdb=" SG CYS A 13 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 551.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 32 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 27 " pdb=" ZN A1202 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A 57 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 61 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 44 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 41 " pdb=" ZN A1203 " pdb="ZN ZN A1203 " - pdb=" NE2 HIS A 92 " pdb="ZN ZN A1203 " - pdb=" NE2 HIS A 97 " pdb="ZN ZN A1203 " - pdb=" SG CYS A 76 " pdb="ZN ZN A1203 " - pdb=" SG CYS A 79 " pdb=" ZN A1204 " pdb="ZN ZN A1204 " - pdb=" NE2 HIS A1003 " pdb="ZN ZN A1204 " - pdb=" SG CYS A 991 " pdb="ZN ZN A1204 " - pdb=" SG CYS A 994 " pdb="ZN ZN A1204 " - pdb=" SG CYS A1008 " Number of angles added : 8 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 56.1% alpha, 8.7% beta 55 base pairs and 99 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 50 through 58 removed outlier: 3.582A pdb=" N VAL A 54 " --> pdb=" O ASN A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 97 through 110 removed outlier: 3.749A pdb=" N GLN A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.622A pdb=" N LEU A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 157 through 171 removed outlier: 4.230A pdb=" N SER A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 267 removed outlier: 3.700A pdb=" N ALA A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.671A pdb=" N GLU A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 304 removed outlier: 5.159A pdb=" N CYS A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.876A pdb=" N ARG A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.692A pdb=" N ASP A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.844A pdb=" N LEU A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LYS A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 385 Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.587A pdb=" N ARG A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 447 through 460 removed outlier: 3.826A pdb=" N ASN A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 496 through 514 removed outlier: 3.663A pdb=" N PHE A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 547 removed outlier: 3.523A pdb=" N LEU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 565 through 576 Processing helix chain 'A' and resid 579 through 590 Processing helix chain 'A' and resid 619 through 640 removed outlier: 4.691A pdb=" N LEU A 623 " --> pdb=" O PRO A 619 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 667 through 684 Processing helix chain 'A' and resid 745 through 759 Processing helix chain 'A' and resid 763 through 775 removed outlier: 3.526A pdb=" N THR A 768 " --> pdb=" O PRO A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 786 removed outlier: 3.582A pdb=" N LEU A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR A 781 " --> pdb=" O PRO A 777 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A 782 " --> pdb=" O ARG A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 808 Processing helix chain 'A' and resid 815 through 821 removed outlier: 4.347A pdb=" N LEU A 819 " --> pdb=" O CYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 826 removed outlier: 3.832A pdb=" N GLY A 826 " --> pdb=" O THR A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 850 Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.623A pdb=" N PHE A 859 " --> pdb=" O MET A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 876 Processing helix chain 'A' and resid 919 through 931 Processing helix chain 'A' and resid 937 through 942 Processing helix chain 'A' and resid 948 through 953 removed outlier: 3.881A pdb=" N GLN A 952 " --> pdb=" O ASN A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 removed outlier: 3.665A pdb=" N THR A 964 " --> pdb=" O ARG A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 983 through 987 Processing helix chain 'A' and resid 1000 through 1007 removed outlier: 3.604A pdb=" N ILE A1005 " --> pdb=" O CYS A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1010 No H-bonds generated for 'chain 'A' and resid 1008 through 1010' Processing helix chain 'A' and resid 1011 through 1033 removed outlier: 3.531A pdb=" N LYS A1033 " --> pdb=" O GLU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1091 removed outlier: 3.651A pdb=" N GLU A1081 " --> pdb=" O SER A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 removed outlier: 3.546A pdb=" N HIS A1099 " --> pdb=" O THR A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1130 removed outlier: 3.950A pdb=" N LEU A1126 " --> pdb=" O ASP A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1168 removed outlier: 3.569A pdb=" N ASP A1154 " --> pdb=" O PHE A1150 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A1168 " --> pdb=" O ARG A1164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 removed outlier: 3.725A pdb=" N TRP A 74 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 495 removed outlier: 7.345A pdb=" N CYS A 469 " --> pdb=" O TYR A 596 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N THR A 598 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR A 471 " --> pdb=" O THR A 598 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 595 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 652 through 655 removed outlier: 3.920A pdb=" N LEU A 659 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS A 693 " --> pdb=" O PHE A 554 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 652 through 655 removed outlier: 3.920A pdb=" N LEU A 659 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS A 693 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A 694 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 643 through 644 removed outlier: 3.633A pdb=" N TYR A 643 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 713 through 714 removed outlier: 3.513A pdb=" N ILE A 714 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 717 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 728 through 730 Processing sheet with id=AA9, first strand: chain 'A' and resid 1036 through 1037 removed outlier: 6.024A pdb=" N ALA A1063 " --> pdb=" O THR A1107 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A1109 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A1065 " --> pdb=" O VAL A1109 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE A1111 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP A1067 " --> pdb=" O PHE A1111 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU A1113 " --> pdb=" O ASP A1067 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR A1069 " --> pdb=" O LEU A1113 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 99 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1921 1.33 - 1.45: 3907 1.45 - 1.57: 6293 1.57 - 1.69: 312 1.69 - 1.82: 71 Bond restraints: 12504 Sorted by residual: bond pdb=" C1' DC T 9 " pdb=" N1 DC T 9 " ideal model delta sigma weight residual 1.468 1.353 0.115 1.40e-02 5.10e+03 6.69e+01 bond pdb=" C1' DC B 61 " pdb=" N1 DC B 61 " ideal model delta sigma weight residual 1.468 1.574 -0.106 1.40e-02 5.10e+03 5.72e+01 bond pdb=" O3B TTP A1206 " pdb=" PG TTP A1206 " ideal model delta sigma weight residual 1.748 1.612 0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C4 DC T 9 " pdb=" N4 DC T 9 " ideal model delta sigma weight residual 1.335 1.280 0.055 9.00e-03 1.23e+04 3.74e+01 bond pdb=" C5 DC T 9 " pdb=" C6 DC T 9 " ideal model delta sigma weight residual 1.339 1.297 0.042 8.00e-03 1.56e+04 2.76e+01 ... (remaining 12499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.50: 17572 8.50 - 17.01: 5 17.01 - 25.51: 3 25.51 - 34.02: 5 34.02 - 42.52: 4 Bond angle restraints: 17589 Sorted by residual: angle pdb=" OP1 DG T 12 " pdb=" P DG T 12 " pdb=" OP2 DG T 12 " ideal model delta sigma weight residual 120.00 77.48 42.52 3.00e+00 1.11e-01 2.01e+02 angle pdb=" OP1 DC B 57 " pdb=" P DC B 57 " pdb=" OP2 DC B 57 " ideal model delta sigma weight residual 120.00 80.08 39.92 3.00e+00 1.11e-01 1.77e+02 angle pdb=" O3' DC T 11 " pdb=" P DG T 12 " pdb=" OP2 DG T 12 " ideal model delta sigma weight residual 108.00 70.89 37.11 3.00e+00 1.11e-01 1.53e+02 angle pdb=" OP2 DC B 57 " pdb=" P DC B 57 " pdb=" O5' DC B 57 " ideal model delta sigma weight residual 108.00 73.50 34.50 3.00e+00 1.11e-01 1.32e+02 angle pdb=" O3' DA B 56 " pdb=" P DC B 57 " pdb=" OP1 DC B 57 " ideal model delta sigma weight residual 108.00 78.06 29.94 3.00e+00 1.11e-01 9.96e+01 ... (remaining 17584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 6610 35.85 - 71.70: 738 71.70 - 107.56: 29 107.56 - 143.41: 2 143.41 - 179.26: 11 Dihedral angle restraints: 7390 sinusoidal: 4244 harmonic: 3146 Sorted by residual: dihedral pdb=" O4' U R 54 " pdb=" C1' U R 54 " pdb=" N1 U R 54 " pdb=" C2 U R 54 " ideal model delta sinusoidal sigma weight residual -128.00 51.26 -179.26 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CD ARG A 166 " pdb=" NE ARG A 166 " pdb=" CZ ARG A 166 " pdb=" NH1 ARG A 166 " ideal model delta sinusoidal sigma weight residual 0.00 60.34 -60.34 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CA ASN A 142 " pdb=" C ASN A 142 " pdb=" N LYS A 143 " pdb=" CA LYS A 143 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 7387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.409: 1995 0.409 - 0.819: 0 0.819 - 1.228: 0 1.228 - 1.638: 0 1.638 - 2.047: 1 Chirality restraints: 1996 Sorted by residual: chirality pdb=" P DT B 35 " pdb=" OP1 DT B 35 " pdb=" OP2 DT B 35 " pdb=" O5' DT B 35 " both_signs ideal model delta sigma weight residual True 2.34 0.29 2.05 2.00e-01 2.50e+01 1.05e+02 chirality pdb=" P DC B 57 " pdb=" OP1 DC B 57 " pdb=" OP2 DC B 57 " pdb=" O5' DC B 57 " both_signs ideal model delta sigma weight residual True 2.34 2.04 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C1' DG B 60 " pdb=" O4' DG B 60 " pdb=" C2' DG B 60 " pdb=" N9 DG B 60 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1993 not shown) Planarity restraints: 1680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 166 " -0.966 9.50e-02 1.11e+02 4.33e-01 1.13e+02 pdb=" NE ARG A 166 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 166 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 166 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 166 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 9 " -0.054 2.00e-02 2.50e+03 3.88e-02 3.38e+01 pdb=" N1 DC T 9 " 0.031 2.00e-02 2.50e+03 pdb=" C2 DC T 9 " 0.031 2.00e-02 2.50e+03 pdb=" O2 DC T 9 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DC T 9 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC T 9 " 0.063 2.00e-02 2.50e+03 pdb=" N4 DC T 9 " -0.067 2.00e-02 2.50e+03 pdb=" C5 DC T 9 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC T 9 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG B 62 " -0.021 2.00e-02 2.50e+03 3.04e-02 2.78e+01 pdb=" N9 DG B 62 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DG B 62 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG B 62 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DG B 62 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG B 62 " 0.061 2.00e-02 2.50e+03 pdb=" O6 DG B 62 " -0.051 2.00e-02 2.50e+03 pdb=" N1 DG B 62 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG B 62 " 0.045 2.00e-02 2.50e+03 pdb=" N2 DG B 62 " -0.044 2.00e-02 2.50e+03 pdb=" N3 DG B 62 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG B 62 " -0.001 2.00e-02 2.50e+03 ... (remaining 1677 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 67 2.46 - 3.07: 7937 3.07 - 3.68: 20016 3.68 - 4.29: 29768 4.29 - 4.90: 45536 Nonbonded interactions: 103324 Sorted by model distance: nonbonded pdb="MG MG A1205 " pdb=" O1A TTP A1206 " model vdw 1.847 2.170 nonbonded pdb=" OG SER A 933 " pdb=" OP1 DA B 31 " model vdw 1.953 3.040 nonbonded pdb=" OH TYR A 257 " pdb=" O PHE A 407 " model vdw 2.011 3.040 nonbonded pdb=" OH TYR A 774 " pdb=" OP2 DG P 20 " model vdw 2.031 3.040 nonbonded pdb=" O VAL A1097 " pdb=" OG1 THR A1101 " model vdw 2.083 3.040 ... (remaining 103319 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=0.65 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.320 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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 0.136 12519 Z= 0.444 Angle : 1.129 42.521 17599 Z= 0.627 Chirality : 0.067 2.047 1996 Planarity : 0.012 0.433 1680 Dihedral : 24.639 179.259 5341 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.71 % Favored : 92.82 % Rotamer: Outliers : 0.63 % Allowed : 21.72 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.26), residues: 1073 helix: -0.02 (0.24), residues: 505 sheet: -2.42 (0.51), residues: 92 loop : -1.61 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 490 TYR 0.018 0.001 TYR A 256 PHE 0.013 0.001 PHE A1150 TRP 0.007 0.001 TRP A 541 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.44 (12504) covalent geometry : angle 1.12482 / 0.63 (17589) SS BOND : bond 0.00242 / 0.13 ( 1) SS BOND : angle 1.61895 / 0.88 ( 2) hydrogen bonds : bond 0.14131 / 8.83 ( 547) hydrogen bonds : angle 6.78496 / 4.84 ( 1481) metal coordination : bond 0.01226 / 0.80 ( 14) metal coordination : angle 4.89862 / 2.45 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 165 ARG cc_start: -0.0412 (OUTLIER) cc_final: -0.1404 (mtm-85) REVERT: A 669 MET cc_start: 0.8956 (tpp) cc_final: 0.8611 (tpp) outliers start: 6 outliers final: 3 residues processed: 87 average time/residue: 0.1315 time to fit residues: 16.0093 Evaluate side-chains 84 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 1101 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0010 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0270 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 overall best weight: 1.9448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.105114 restraints weight = 18826.145| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.84 r_work: 0.3189 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12519 Z= 0.225 Angle : 1.075 41.386 17599 Z= 0.480 Chirality : 0.068 1.990 1996 Planarity : 0.006 0.092 1680 Dihedral : 26.201 177.342 3142 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.78 % Favored : 93.85 % Rotamer: Outliers : 3.25 % Allowed : 21.09 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.26), residues: 1073 helix: 0.10 (0.23), residues: 533 sheet: -2.24 (0.48), residues: 94 loop : -1.43 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 165 TYR 0.017 0.002 TYR A 377 PHE 0.015 0.002 PHE A1159 TRP 0.027 0.002 TRP A 489 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (12504) covalent geometry : angle 1.07337 / 0.48 (17589) SS BOND : bond 0.00036 / 0.02 ( 1) SS BOND : angle 1.30364 / 0.72 ( 2) hydrogen bonds : bond 0.06258 / 4.11 ( 547) hydrogen bonds : angle 4.93692 / 3.52 ( 1481) metal coordination : bond 0.01433 / 1.03 ( 14) metal coordination : angle 3.31544 / 1.71 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 291 ASN cc_start: 0.7496 (m-40) cc_final: 0.7190 (m-40) REVERT: A 329 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7181 (mm-40) REVERT: A 377 TYR cc_start: 0.8123 (t80) cc_final: 0.7914 (t80) REVERT: A 465 MET cc_start: 0.8247 (ptm) cc_final: 0.7901 (ptt) REVERT: A 691 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8306 (mmmt) REVERT: A 989 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8189 (mtmt) outliers start: 31 outliers final: 10 residues processed: 108 average time/residue: 0.1397 time to fit residues: 20.9554 Evaluate side-chains 90 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 112 optimal weight: 10.0000 chunk 86 optimal weight: 0.0770 chunk 118 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS A 670 ASN A1099 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.148511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108626 restraints weight = 19013.523| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.84 r_work: 0.3240 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12519 Z= 0.147 Angle : 0.873 40.046 17599 Z= 0.409 Chirality : 0.066 2.155 1996 Planarity : 0.005 0.069 1680 Dihedral : 25.966 179.714 3137 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.57 % Favored : 95.06 % Rotamer: Outliers : 2.62 % Allowed : 22.25 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.26), residues: 1073 helix: 0.47 (0.23), residues: 524 sheet: -1.93 (0.49), residues: 95 loop : -1.30 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 956 TYR 0.014 0.001 TYR A 256 PHE 0.014 0.001 PHE A1150 TRP 0.013 0.001 TRP A 489 HIS 0.009 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (12504) covalent geometry : angle 0.87123 / 0.41 (17589) SS BOND : bond 0.00164 / 0.09 ( 1) SS BOND : angle 1.18974 / 0.66 ( 2) hydrogen bonds : bond 0.05545 / 3.63 ( 547) hydrogen bonds : angle 4.68037 / 3.32 ( 1481) metal coordination : bond 0.00464 / 0.30 ( 14) metal coordination : angle 2.53837 / 1.22 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8133 (mp0) cc_final: 0.7840 (mp0) REVERT: A 291 ASN cc_start: 0.7421 (m-40) cc_final: 0.7185 (m-40) REVERT: A 329 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7105 (mm-40) REVERT: A 441 LYS cc_start: 0.8234 (mmpt) cc_final: 0.7680 (tttt) REVERT: A 465 MET cc_start: 0.8233 (ptm) cc_final: 0.7910 (ptt) REVERT: A 691 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8509 (mmmt) REVERT: A 736 ASP cc_start: 0.8968 (t0) cc_final: 0.8747 (t70) outliers start: 25 outliers final: 12 residues processed: 103 average time/residue: 0.1220 time to fit residues: 17.7222 Evaluate side-chains 93 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 89 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 114 optimal weight: 20.0000 chunk 31 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 67 optimal weight: 0.0980 chunk 83 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.149492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109466 restraints weight = 18974.585| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.88 r_work: 0.3254 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12519 Z= 0.140 Angle : 0.856 40.133 17599 Z= 0.398 Chirality : 0.067 2.250 1996 Planarity : 0.004 0.048 1680 Dihedral : 25.740 178.095 3137 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.75 % Favored : 94.97 % Rotamer: Outliers : 2.31 % Allowed : 23.71 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.26), residues: 1073 helix: 0.66 (0.23), residues: 526 sheet: -1.67 (0.49), residues: 93 loop : -1.25 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 956 TYR 0.023 0.001 TYR A 377 PHE 0.012 0.001 PHE A1159 TRP 0.008 0.001 TRP A 124 HIS 0.003 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (12504) covalent geometry : angle 0.85491 / 0.40 (17589) SS BOND : bond 0.00176 / 0.09 ( 1) SS BOND : angle 1.17089 / 0.65 ( 2) hydrogen bonds : bond 0.05020 / 3.29 ( 547) hydrogen bonds : angle 4.40450 / 3.13 ( 1481) metal coordination : bond 0.00411 / 0.28 ( 14) metal coordination : angle 2.02559 / 0.97 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7420 (mmt) cc_final: 0.7193 (tpt) REVERT: A 26 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7979 (mm-30) REVERT: A 77 GLU cc_start: 0.8115 (mp0) cc_final: 0.7763 (mp0) REVERT: A 329 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7127 (mm-40) REVERT: A 441 LYS cc_start: 0.8205 (mmpt) cc_final: 0.7500 (mptt) REVERT: A 465 MET cc_start: 0.8236 (ptm) cc_final: 0.7922 (ptt) REVERT: A 691 LYS cc_start: 0.8891 (mmtt) cc_final: 0.8551 (mmmt) outliers start: 22 outliers final: 14 residues processed: 104 average time/residue: 0.1195 time to fit residues: 17.6081 Evaluate side-chains 98 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106638 restraints weight = 18753.407| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.88 r_work: 0.3202 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12519 Z= 0.187 Angle : 0.872 40.152 17599 Z= 0.404 Chirality : 0.065 2.079 1996 Planarity : 0.005 0.051 1680 Dihedral : 25.595 176.391 3135 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.94 % Favored : 94.87 % Rotamer: Outliers : 3.04 % Allowed : 24.34 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.26), residues: 1073 helix: 0.59 (0.23), residues: 535 sheet: -1.63 (0.49), residues: 95 loop : -1.24 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 490 TYR 0.011 0.002 TYR A 953 PHE 0.014 0.002 PHE A1159 TRP 0.008 0.001 TRP A1035 HIS 0.004 0.001 HIS A 959 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (12504) covalent geometry : angle 0.87145 / 0.40 (17589) SS BOND : bond 0.00102 / 0.05 ( 1) SS BOND : angle 1.13194 / 0.63 ( 2) hydrogen bonds : bond 0.04991 / 3.31 ( 547) hydrogen bonds : angle 4.37216 / 3.11 ( 1481) metal coordination : bond 0.01247 / 0.92 ( 14) metal coordination : angle 2.03267 / 1.00 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8091 (mp0) cc_final: 0.7699 (mp0) REVERT: A 329 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7052 (mm-40) REVERT: A 465 MET cc_start: 0.8230 (ptm) cc_final: 0.7869 (ptm) REVERT: A 691 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8610 (mmmt) REVERT: A 743 ARG cc_start: 0.7093 (ttm-80) cc_final: 0.6863 (ttm-80) REVERT: A 989 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.7970 (mtmt) outliers start: 29 outliers final: 15 residues processed: 107 average time/residue: 0.1129 time to fit residues: 17.2803 Evaluate side-chains 99 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 89 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 63 optimal weight: 0.0470 chunk 81 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1012 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.148092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.107763 restraints weight = 18880.776| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.90 r_work: 0.3224 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12519 Z= 0.153 Angle : 0.850 40.083 17599 Z= 0.392 Chirality : 0.065 2.156 1996 Planarity : 0.004 0.047 1680 Dihedral : 25.508 176.129 3135 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.94 % Favored : 94.87 % Rotamer: Outliers : 3.04 % Allowed : 24.24 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.26), residues: 1073 helix: 0.74 (0.23), residues: 538 sheet: -1.53 (0.50), residues: 97 loop : -1.24 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 490 TYR 0.014 0.001 TYR A 256 PHE 0.012 0.001 PHE A1159 TRP 0.007 0.001 TRP A1035 HIS 0.003 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (12504) covalent geometry : angle 0.84914 / 0.39 (17589) SS BOND : bond 0.00109 / 0.06 ( 1) SS BOND : angle 1.05280 / 0.59 ( 2) hydrogen bonds : bond 0.04679 / 3.10 ( 547) hydrogen bonds : angle 4.23836 / 3.00 ( 1481) metal coordination : bond 0.00759 / 0.54 ( 14) metal coordination : angle 1.91298 / 0.91 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7444 (mmt) cc_final: 0.7102 (tpt) REVERT: A 26 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8031 (mm-30) REVERT: A 77 GLU cc_start: 0.8077 (mp0) cc_final: 0.7673 (mp0) REVERT: A 329 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7024 (mm-40) REVERT: A 408 ARG cc_start: 0.8074 (mmm-85) cc_final: 0.7794 (mmm-85) REVERT: A 441 LYS cc_start: 0.7995 (mmpt) cc_final: 0.7215 (mptt) REVERT: A 465 MET cc_start: 0.8215 (ptm) cc_final: 0.7856 (ptm) REVERT: A 490 ARG cc_start: 0.6294 (ttt90) cc_final: 0.6059 (ttt180) REVERT: A 691 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8626 (mmmt) REVERT: A 743 ARG cc_start: 0.7049 (ttm-80) cc_final: 0.6808 (mtm-85) REVERT: A 989 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7905 (mtmt) outliers start: 29 outliers final: 21 residues processed: 104 average time/residue: 0.1262 time to fit residues: 18.3367 Evaluate side-chains 105 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 37 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.146234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105912 restraints weight = 18698.773| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.86 r_work: 0.3191 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12519 Z= 0.197 Angle : 0.871 40.137 17599 Z= 0.401 Chirality : 0.065 2.090 1996 Planarity : 0.005 0.046 1680 Dihedral : 25.422 175.753 3135 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.13 % Favored : 94.69 % Rotamer: Outliers : 3.15 % Allowed : 24.45 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.26), residues: 1073 helix: 0.73 (0.22), residues: 540 sheet: -1.47 (0.51), residues: 97 loop : -1.25 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 490 TYR 0.012 0.002 TYR A 256 PHE 0.014 0.002 PHE A1159 TRP 0.008 0.001 TRP A1035 HIS 0.005 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (12504) covalent geometry : angle 0.87024 / 0.40 (17589) SS BOND : bond 0.00042 / 0.02 ( 1) SS BOND : angle 1.00302 / 0.56 ( 2) hydrogen bonds : bond 0.04760 / 3.19 ( 547) hydrogen bonds : angle 4.26280 / 3.02 ( 1481) metal coordination : bond 0.01387 / 1.01 ( 14) metal coordination : angle 1.99423 / 0.99 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8896 (mt) cc_final: 0.8622 (mt) REVERT: A 26 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8063 (mm-30) REVERT: A 77 GLU cc_start: 0.8067 (mp0) cc_final: 0.7643 (mp0) REVERT: A 329 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7125 (mm-40) REVERT: A 408 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7784 (mmm-85) REVERT: A 485 ASP cc_start: 0.7353 (t0) cc_final: 0.7112 (t0) REVERT: A 691 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8631 (mmmt) REVERT: A 989 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.7983 (mtmt) REVERT: A 1089 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7798 (pttt) outliers start: 30 outliers final: 19 residues processed: 105 average time/residue: 0.1294 time to fit residues: 19.1414 Evaluate side-chains 101 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1089 LYS Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 86 optimal weight: 0.3980 chunk 4 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 116 optimal weight: 40.0000 chunk 93 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 574 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.148090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107874 restraints weight = 18687.665| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.89 r_work: 0.3225 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12519 Z= 0.143 Angle : 0.842 40.031 17599 Z= 0.387 Chirality : 0.065 2.155 1996 Planarity : 0.004 0.045 1680 Dihedral : 25.324 176.372 3135 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.94 % Favored : 94.87 % Rotamer: Outliers : 3.15 % Allowed : 24.24 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.26), residues: 1073 helix: 0.93 (0.23), residues: 540 sheet: -1.29 (0.52), residues: 97 loop : -1.22 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 490 TYR 0.010 0.001 TYR A 256 PHE 0.011 0.001 PHE A1159 TRP 0.007 0.001 TRP A1035 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (12504) covalent geometry : angle 0.84134 / 0.39 (17589) SS BOND : bond 0.00109 / 0.06 ( 1) SS BOND : angle 1.01492 / 0.57 ( 2) hydrogen bonds : bond 0.04422 / 2.96 ( 547) hydrogen bonds : angle 4.14320 / 2.93 ( 1481) metal coordination : bond 0.00610 / 0.43 ( 14) metal coordination : angle 1.85680 / 0.89 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8030 (mm-30) REVERT: A 77 GLU cc_start: 0.8075 (mp0) cc_final: 0.7660 (mp0) REVERT: A 329 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7056 (mm-40) REVERT: A 353 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8386 (mtm180) REVERT: A 408 ARG cc_start: 0.8094 (mmm-85) cc_final: 0.7743 (mmm-85) REVERT: A 432 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7634 (p0) REVERT: A 441 LYS cc_start: 0.8018 (mmpt) cc_final: 0.7224 (mptt) REVERT: A 485 ASP cc_start: 0.7451 (t0) cc_final: 0.7229 (t0) REVERT: A 556 ASP cc_start: 0.7640 (t0) cc_final: 0.7340 (m-30) REVERT: A 691 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8406 (mmmt) REVERT: A 743 ARG cc_start: 0.7156 (mtm-85) cc_final: 0.6936 (mtm-85) REVERT: A 1089 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7779 (pttt) outliers start: 30 outliers final: 20 residues processed: 110 average time/residue: 0.1274 time to fit residues: 19.6407 Evaluate side-chains 102 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1089 LYS Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 94 optimal weight: 0.0970 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 0.0040 chunk 26 optimal weight: 0.9980 overall best weight: 1.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.146577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106192 restraints weight = 18850.676| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.87 r_work: 0.3194 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12519 Z= 0.184 Angle : 0.865 40.087 17599 Z= 0.397 Chirality : 0.065 2.096 1996 Planarity : 0.005 0.046 1680 Dihedral : 25.313 176.376 3135 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.31 % Favored : 94.50 % Rotamer: Outliers : 2.73 % Allowed : 24.45 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.26), residues: 1073 helix: 0.85 (0.23), residues: 543 sheet: -1.27 (0.51), residues: 97 loop : -1.29 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 490 TYR 0.011 0.002 TYR A 953 PHE 0.010 0.002 PHE A 925 TRP 0.011 0.001 TRP A 489 HIS 0.005 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (12504) covalent geometry : angle 0.86426 / 0.40 (17589) SS BOND : bond 0.00082 / 0.04 ( 1) SS BOND : angle 1.05394 / 0.59 ( 2) hydrogen bonds : bond 0.04557 / 3.07 ( 547) hydrogen bonds : angle 4.18964 / 2.98 ( 1481) metal coordination : bond 0.01237 / 0.90 ( 14) metal coordination : angle 1.93023 / 0.94 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8880 (mt) cc_final: 0.8607 (mt) REVERT: A 26 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8042 (mm-30) REVERT: A 77 GLU cc_start: 0.8073 (mp0) cc_final: 0.7649 (mp0) REVERT: A 329 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7101 (mm-40) REVERT: A 408 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7736 (mmm-85) REVERT: A 441 LYS cc_start: 0.8042 (mmpt) cc_final: 0.7245 (mptt) REVERT: A 485 ASP cc_start: 0.7491 (t0) cc_final: 0.7258 (t0) REVERT: A 556 ASP cc_start: 0.7658 (t0) cc_final: 0.7328 (m-30) REVERT: A 691 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8419 (mmmt) REVERT: A 743 ARG cc_start: 0.7150 (mtm-85) cc_final: 0.6938 (mtm-85) REVERT: A 989 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7969 (mtmt) REVERT: A 1089 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7797 (pttt) outliers start: 26 outliers final: 20 residues processed: 100 average time/residue: 0.1294 time to fit residues: 17.9741 Evaluate side-chains 103 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1089 LYS Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 31 optimal weight: 0.3980 chunk 60 optimal weight: 4.9990 chunk 5 optimal weight: 0.0970 chunk 97 optimal weight: 0.0370 chunk 74 optimal weight: 0.9980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.148968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108863 restraints weight = 18915.621| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.91 r_work: 0.3240 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 12519 Z= 0.127 Angle : 0.837 39.973 17599 Z= 0.384 Chirality : 0.065 2.171 1996 Planarity : 0.004 0.045 1680 Dihedral : 25.219 176.971 3135 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.94 % Favored : 94.87 % Rotamer: Outliers : 1.99 % Allowed : 24.97 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.26), residues: 1073 helix: 1.08 (0.23), residues: 541 sheet: -1.07 (0.52), residues: 95 loop : -1.24 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 490 TYR 0.009 0.001 TYR A 953 PHE 0.026 0.001 PHE A 298 TRP 0.009 0.001 TRP A 489 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 (12504) covalent geometry : angle 0.83667 / 0.38 (17589) SS BOND : bond 0.00121 / 0.06 ( 1) SS BOND : angle 1.05748 / 0.59 ( 2) hydrogen bonds : bond 0.04258 / 2.86 ( 547) hydrogen bonds : angle 4.08385 / 2.89 ( 1481) metal coordination : bond 0.00287 / 0.19 ( 14) metal coordination : angle 1.83751 / 0.88 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8852 (mt) cc_final: 0.8509 (mt) REVERT: A 26 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8016 (mm-30) REVERT: A 77 GLU cc_start: 0.8075 (mp0) cc_final: 0.7690 (mp0) REVERT: A 329 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7076 (mm-40) REVERT: A 408 ARG cc_start: 0.8090 (mmm-85) cc_final: 0.7783 (mmm-85) REVERT: A 441 LYS cc_start: 0.7943 (mmpt) cc_final: 0.7156 (mptt) REVERT: A 485 ASP cc_start: 0.7443 (t0) cc_final: 0.7227 (t0) REVERT: A 556 ASP cc_start: 0.7602 (t0) cc_final: 0.7378 (m-30) REVERT: A 691 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8407 (mmmt) REVERT: A 743 ARG cc_start: 0.7118 (mtm-85) cc_final: 0.6901 (mtm-85) outliers start: 19 outliers final: 14 residues processed: 100 average time/residue: 0.1264 time to fit residues: 17.5266 Evaluate side-chains 99 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 22 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.0670 chunk 74 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.147805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107535 restraints weight = 18947.781| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.90 r_work: 0.3218 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12519 Z= 0.157 Angle : 0.851 40.052 17599 Z= 0.389 Chirality : 0.064 2.119 1996 Planarity : 0.004 0.046 1680 Dihedral : 25.152 176.854 3133 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.31 % Favored : 94.50 % Rotamer: Outliers : 1.99 % Allowed : 25.18 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.26), residues: 1073 helix: 1.04 (0.23), residues: 539 sheet: -1.09 (0.51), residues: 95 loop : -1.18 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 490 TYR 0.010 0.001 TYR A 953 PHE 0.010 0.001 PHE A 625 TRP 0.007 0.001 TRP A 489 HIS 0.005 0.001 HIS A 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (12504) covalent geometry : angle 0.85014 / 0.39 (17589) SS BOND : bond 0.00105 / 0.06 ( 1) SS BOND : angle 1.12488 / 0.63 ( 2) hydrogen bonds : bond 0.04340 / 2.94 ( 547) hydrogen bonds : angle 4.13620 / 2.93 ( 1481) metal coordination : bond 0.00868 / 0.63 ( 14) metal coordination : angle 1.75170 / 0.84 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3833.58 seconds wall clock time: 66 minutes 9.93 seconds (3969.93 seconds total)