Starting phenix.real_space_refine on Wed Jul 30 01:23:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nl3_49516/07_2025/9nl3_49516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nl3_49516/07_2025/9nl3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9nl3_49516/07_2025/9nl3_49516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nl3_49516/07_2025/9nl3_49516.map" model { file = "/net/cci-nas-00/data/ceres_data/9nl3_49516/07_2025/9nl3_49516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nl3_49516/07_2025/9nl3_49516.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.07, per 1000 atoms: 0.68 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: 3.37 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 5.19 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: 6.73 Time building geometry restraints manager: 4.01 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 1.490 1.353 0.137 3.00e-02 1.11e+03 2.07e+01 bond pdb=" C4 DC T 9 " pdb=" N4 DC T 9 " ideal model delta sigma weight residual 1.337 1.280 0.057 2.00e-02 2.50e+03 8.13e+00 bond pdb=" C1' DC B 61 " pdb=" N1 DC B 61 " ideal model delta sigma weight residual 1.490 1.574 -0.084 3.00e-02 1.11e+03 7.81e+00 bond pdb=" N HIS A 52 " pdb=" CA HIS A 52 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.25e-02 6.40e+03 6.40e+00 bond pdb=" N ARG A 166 " pdb=" CA ARG A 166 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.24e-02 6.50e+03 5.73e+00 ... (remaining 12499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.50: 17575 8.50 - 17.01: 2 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: 6600 35.85 - 71.70: 723 71.70 - 107.56: 29 107.56 - 143.41: 3 143.41 - 179.26: 11 Dihedral angle restraints: 7366 sinusoidal: 4220 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=" C2 TTP A1206 " pdb=" C1' TTP A1206 " pdb=" N1 TTP A1206 " pdb=" O4' TTP A1206 " ideal model delta sinusoidal sigma weight residual 301.68 158.68 143.00 1 2.00e+01 2.50e-03 4.32e+01 ... (remaining 7363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.412: 1995 0.412 - 0.823: 0 0.823 - 1.235: 0 1.235 - 1.646: 0 1.646 - 2.058: 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 2.35 0.29 2.06 2.00e-01 2.50e+01 1.06e+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 2.35 2.04 0.30 2.00e-01 2.50e+01 2.27e+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 2.42 2.21 0.21 2.00e-01 2.50e+01 1.14e+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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 40.280 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 12519 Z= 0.208 Angle : 1.061 42.521 17599 Z= 0.471 Chirality : 0.062 2.058 1996 Planarity : 0.012 0.433 1680 Dihedral : 24.599 179.259 5317 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.14 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.26), 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 TRP 0.007 0.001 TRP A 541 HIS 0.006 0.001 HIS A 52 PHE 0.013 0.001 PHE A1150 TYR 0.018 0.001 TYR A 256 ARG 0.005 0.001 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.14131 ( 547) hydrogen bonds : angle 6.78496 ( 1481) metal coordination : bond 0.01226 ( 14) metal coordination : angle 4.89862 ( 8) SS BOND : bond 0.00242 ( 1) SS BOND : angle 1.61895 ( 2) covalent geometry : bond 0.00462 (12504) covalent geometry : angle 1.05636 (17589) *********************** 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 : 1.188 Fit side-chains revert: symmetry clash REVERT: A 165 ARG cc_start: -0.0412 (OUTLIER) cc_final: -0.1120 (ptp90) REVERT: A 669 MET cc_start: 0.8956 (tpp) cc_final: 0.8612 (tpp) outliers start: 6 outliers final: 3 residues processed: 87 average time/residue: 0.2969 time to fit residues: 36.3139 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 : 1.152 ------------------------------------------------------------------------------- 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 102 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 94 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 670 ASN A 993 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.150241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110688 restraints weight = 18688.805| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.90 r_work: 0.3268 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12519 Z= 0.158 Angle : 0.832 39.839 17599 Z= 0.387 Chirality : 0.040 0.302 1996 Planarity : 0.005 0.042 1680 Dihedral : 25.893 178.948 3118 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.75 % Favored : 94.87 % Rotamer: Outliers : 2.41 % Allowed : 21.51 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.26), residues: 1073 helix: 0.38 (0.23), residues: 536 sheet: -1.83 (0.52), residues: 85 loop : -1.43 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 489 HIS 0.006 0.001 HIS A1019 PHE 0.012 0.001 PHE A1159 TYR 0.015 0.002 TYR A 377 ARG 0.009 0.001 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.05245 ( 547) hydrogen bonds : angle 4.62010 ( 1481) metal coordination : bond 0.00800 ( 14) metal coordination : angle 3.17119 ( 8) SS BOND : bond 0.00146 ( 1) SS BOND : angle 1.58752 ( 2) covalent geometry : bond 0.00349 (12504) covalent geometry : angle 0.82890 (17589) *********************** 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 114 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 165 ARG cc_start: -0.0854 (OUTLIER) cc_final: -0.1095 (ptp90) REVERT: A 329 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6804 (mm-40) REVERT: A 550 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8705 (tp) REVERT: A 691 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8327 (mmmt) REVERT: A 986 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7536 (mm110) outliers start: 23 outliers final: 9 residues processed: 109 average time/residue: 0.2877 time to fit residues: 43.6723 Evaluate side-chains 92 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 329 GLN 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 550 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 986 GLN 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 100 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 72 optimal weight: 0.0570 chunk 62 optimal weight: 0.0370 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 720 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.148839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108482 restraints weight = 18853.130| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.97 r_work: 0.3232 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12519 Z= 0.163 Angle : 0.804 39.969 17599 Z= 0.370 Chirality : 0.039 0.262 1996 Planarity : 0.005 0.046 1680 Dihedral : 25.591 179.262 3117 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.85 % Favored : 94.87 % Rotamer: Outliers : 2.73 % Allowed : 22.35 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.26), residues: 1073 helix: 0.54 (0.23), residues: 532 sheet: -1.68 (0.51), residues: 93 loop : -1.25 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 489 HIS 0.003 0.001 HIS A1099 PHE 0.013 0.002 PHE A1159 TYR 0.010 0.001 TYR A 953 ARG 0.013 0.001 ARG A 956 Details of bonding type rmsd hydrogen bonds : bond 0.04862 ( 547) hydrogen bonds : angle 4.45497 ( 1481) metal coordination : bond 0.00826 ( 14) metal coordination : angle 2.27695 ( 8) SS BOND : bond 0.00133 ( 1) SS BOND : angle 1.22247 ( 2) covalent geometry : bond 0.00366 (12504) covalent geometry : angle 0.80217 (17589) *********************** 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 110 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7444 (mmt) cc_final: 0.7117 (tpt) REVERT: A 77 GLU cc_start: 0.8114 (mp0) cc_final: 0.7738 (mp0) REVERT: A 329 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6898 (mm-40) REVERT: A 377 TYR cc_start: 0.7894 (t80) cc_final: 0.7649 (t80) REVERT: A 441 LYS cc_start: 0.8005 (mmpt) cc_final: 0.7390 (mptt) REVERT: A 465 MET cc_start: 0.8236 (ptm) cc_final: 0.7928 (ptt) REVERT: A 600 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8337 (tttp) REVERT: A 691 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8387 (mmmt) REVERT: A 986 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7581 (mm110) REVERT: A 989 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7903 (mtmt) outliers start: 26 outliers final: 13 residues processed: 103 average time/residue: 0.3007 time to fit residues: 42.7603 Evaluate side-chains 95 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 1.815 ------------------------------------------------------------------------------- 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 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 432 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 986 GLN Chi-restraints excluded: chain A residue 989 LYS 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 82 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1099 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.149843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109962 restraints weight = 18789.752| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.91 r_work: 0.3257 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12519 Z= 0.142 Angle : 0.791 40.029 17599 Z= 0.362 Chirality : 0.038 0.247 1996 Planarity : 0.004 0.047 1680 Dihedral : 25.401 178.686 3113 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.85 % Favored : 94.97 % Rotamer: Outliers : 2.62 % Allowed : 23.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.26), residues: 1073 helix: 0.73 (0.23), residues: 535 sheet: -1.52 (0.50), residues: 95 loop : -1.20 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1035 HIS 0.004 0.001 HIS A1099 PHE 0.012 0.001 PHE A1159 TYR 0.010 0.001 TYR A 257 ARG 0.004 0.000 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 547) hydrogen bonds : angle 4.30731 ( 1481) metal coordination : bond 0.00513 ( 14) metal coordination : angle 1.93089 ( 8) SS BOND : bond 0.00142 ( 1) SS BOND : angle 1.12874 ( 2) covalent geometry : bond 0.00318 (12504) covalent geometry : angle 0.79043 (17589) *********************** 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 105 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7371 (mmt) cc_final: 0.7019 (tpt) REVERT: A 26 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8066 (mm-30) REVERT: A 77 GLU cc_start: 0.8072 (mp0) cc_final: 0.7672 (mp0) REVERT: A 329 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6944 (mm-40) REVERT: A 377 TYR cc_start: 0.7924 (t80) cc_final: 0.7663 (t80) REVERT: A 441 LYS cc_start: 0.8019 (mmpt) cc_final: 0.7408 (mptt) REVERT: A 465 MET cc_start: 0.8232 (ptm) cc_final: 0.7921 (ptt) REVERT: A 490 ARG cc_start: 0.6349 (ttt90) cc_final: 0.6108 (ttt180) REVERT: A 600 LYS cc_start: 0.8770 (ttmt) cc_final: 0.8316 (tttp) REVERT: A 691 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8409 (mmmt) REVERT: A 986 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7558 (mm110) outliers start: 25 outliers final: 12 residues processed: 99 average time/residue: 0.3771 time to fit residues: 53.9265 Evaluate side-chains 94 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 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 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 986 GLN 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 62 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 31 optimal weight: 0.0670 chunk 30 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 79 optimal weight: 0.0980 chunk 89 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1099 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.150981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111179 restraints weight = 18941.698| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.90 r_work: 0.3277 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12519 Z= 0.132 Angle : 0.774 40.017 17599 Z= 0.352 Chirality : 0.037 0.225 1996 Planarity : 0.004 0.043 1680 Dihedral : 25.128 179.541 3111 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.22 % Favored : 94.59 % Rotamer: Outliers : 2.62 % Allowed : 23.92 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1073 helix: 0.97 (0.23), residues: 540 sheet: -1.32 (0.51), residues: 97 loop : -1.15 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 124 HIS 0.010 0.001 HIS A1099 PHE 0.014 0.001 PHE A 139 TYR 0.009 0.001 TYR A 953 ARG 0.004 0.000 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 547) hydrogen bonds : angle 4.08501 ( 1481) metal coordination : bond 0.00437 ( 14) metal coordination : angle 1.80492 ( 8) SS BOND : bond 0.00134 ( 1) SS BOND : angle 1.15162 ( 2) covalent geometry : bond 0.00293 (12504) covalent geometry : angle 0.77346 (17589) *********************** 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 116 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8820 (mt) cc_final: 0.8545 (mt) REVERT: A 26 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8057 (mm-30) REVERT: A 353 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8282 (mtm180) REVERT: A 377 TYR cc_start: 0.7902 (t80) cc_final: 0.7578 (t80) REVERT: A 432 ASP cc_start: 0.7771 (p0) cc_final: 0.7280 (p0) REVERT: A 441 LYS cc_start: 0.7961 (mmpt) cc_final: 0.7340 (mptt) REVERT: A 465 MET cc_start: 0.8159 (ptm) cc_final: 0.7842 (ptt) REVERT: A 600 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8292 (tttp) REVERT: A 669 MET cc_start: 0.8730 (tpp) cc_final: 0.8525 (tpp) REVERT: A 691 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8467 (mmmt) REVERT: A 856 MET cc_start: 0.8404 (tmm) cc_final: 0.8177 (tmm) REVERT: A 986 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7603 (mm110) REVERT: A 989 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.7840 (mtmt) outliers start: 25 outliers final: 13 residues processed: 109 average time/residue: 0.2961 time to fit residues: 45.1121 Evaluate side-chains 99 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain A residue 301 LEU 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 597 ILE 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 986 GLN Chi-restraints excluded: chain A residue 989 LYS 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 92 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 89 optimal weight: 0.2980 chunk 37 optimal weight: 0.0870 chunk 7 optimal weight: 20.0000 chunk 80 optimal weight: 0.0000 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 overall best weight: 0.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN A1099 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.150178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110120 restraints weight = 19027.037| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.90 r_work: 0.3260 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12519 Z= 0.144 Angle : 0.776 39.966 17599 Z= 0.352 Chirality : 0.037 0.217 1996 Planarity : 0.004 0.040 1680 Dihedral : 25.058 179.012 3111 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.57 % Favored : 95.25 % Rotamer: Outliers : 2.73 % Allowed : 24.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1073 helix: 1.08 (0.23), residues: 547 sheet: -1.10 (0.52), residues: 95 loop : -1.18 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 489 HIS 0.007 0.001 HIS A1099 PHE 0.010 0.001 PHE A1159 TYR 0.010 0.001 TYR A 953 ARG 0.006 0.000 ARG A1062 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 547) hydrogen bonds : angle 4.01320 ( 1481) metal coordination : bond 0.00671 ( 14) metal coordination : angle 1.72702 ( 8) SS BOND : bond 0.00142 ( 1) SS BOND : angle 1.10423 ( 2) covalent geometry : bond 0.00328 (12504) covalent geometry : angle 0.77548 (17589) *********************** 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 113 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8832 (mt) cc_final: 0.8536 (mt) REVERT: A 26 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 329 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6938 (mm-40) REVERT: A 353 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8370 (mtm180) REVERT: A 377 TYR cc_start: 0.7811 (t80) cc_final: 0.7368 (t80) REVERT: A 432 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7585 (p0) REVERT: A 441 LYS cc_start: 0.7937 (mmpt) cc_final: 0.7318 (mptt) REVERT: A 465 MET cc_start: 0.8184 (ptm) cc_final: 0.7845 (ptm) REVERT: A 600 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8261 (tttp) REVERT: A 669 MET cc_start: 0.8798 (tpp) cc_final: 0.8595 (tpp) REVERT: A 691 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8481 (mmmt) REVERT: A 986 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7569 (mm110) REVERT: A 989 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7846 (mtmt) outliers start: 26 outliers final: 11 residues processed: 106 average time/residue: 0.2918 time to fit residues: 43.4631 Evaluate side-chains 98 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain A residue 286 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 432 ASP Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 608 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 986 GLN Chi-restraints excluded: chain A residue 989 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 37 optimal weight: 0.0030 chunk 112 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1012 GLN A1099 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.149839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109677 restraints weight = 18831.541| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.89 r_work: 0.3255 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12519 Z= 0.149 Angle : 0.777 39.767 17599 Z= 0.353 Chirality : 0.037 0.203 1996 Planarity : 0.004 0.040 1680 Dihedral : 25.035 179.355 3111 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.94 % Favored : 94.87 % Rotamer: Outliers : 2.83 % Allowed : 24.03 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1073 helix: 1.09 (0.23), residues: 548 sheet: -1.06 (0.51), residues: 95 loop : -1.16 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 489 HIS 0.009 0.001 HIS A1099 PHE 0.009 0.001 PHE A1159 TYR 0.009 0.001 TYR A 953 ARG 0.006 0.000 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 547) hydrogen bonds : angle 3.98861 ( 1481) metal coordination : bond 0.00743 ( 14) metal coordination : angle 1.76012 ( 8) SS BOND : bond 0.00125 ( 1) SS BOND : angle 1.09153 ( 2) covalent geometry : bond 0.00338 (12504) covalent geometry : angle 0.77637 (17589) *********************** 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 112 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8832 (mt) cc_final: 0.8529 (mt) REVERT: A 26 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 329 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.7037 (mm-40) REVERT: A 353 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8377 (mtm180) REVERT: A 377 TYR cc_start: 0.7867 (t80) cc_final: 0.7358 (t80) REVERT: A 434 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8520 (mp) REVERT: A 441 LYS cc_start: 0.7961 (mmpt) cc_final: 0.7345 (mptt) REVERT: A 490 ARG cc_start: 0.6179 (ttt90) cc_final: 0.5929 (ttt180) REVERT: A 600 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8276 (tttp) REVERT: A 691 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8486 (mmmt) REVERT: A 856 MET cc_start: 0.8192 (tmm) cc_final: 0.7698 (tmm) REVERT: A 986 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7590 (mm110) REVERT: A 989 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7863 (mtmt) outliers start: 27 outliers final: 11 residues processed: 105 average time/residue: 0.3988 time to fit residues: 58.1101 Evaluate side-chains 98 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 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 434 ILE Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 630 ASP 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 986 GLN Chi-restraints excluded: chain A residue 989 LYS 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 120 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 47 optimal weight: 0.0070 chunk 13 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1099 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.150492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110426 restraints weight = 18963.904| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.91 r_work: 0.3264 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2560 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= 0.135 Angle : 0.774 39.785 17599 Z= 0.351 Chirality : 0.037 0.190 1996 Planarity : 0.004 0.039 1680 Dihedral : 24.946 179.732 3109 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.29 % Favored : 95.53 % Rotamer: Outliers : 2.41 % Allowed : 24.03 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1073 helix: 1.17 (0.23), residues: 549 sheet: -0.99 (0.52), residues: 95 loop : -1.10 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1035 HIS 0.005 0.001 HIS A1099 PHE 0.019 0.001 PHE A 298 TYR 0.009 0.001 TYR A 953 ARG 0.005 0.000 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 547) hydrogen bonds : angle 3.93220 ( 1481) metal coordination : bond 0.00486 ( 14) metal coordination : angle 1.73447 ( 8) SS BOND : bond 0.00147 ( 1) SS BOND : angle 1.10154 ( 2) covalent geometry : bond 0.00303 (12504) covalent geometry : angle 0.77279 (17589) *********************** 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 114 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8824 (mt) cc_final: 0.8530 (mt) REVERT: A 26 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7914 (mm-30) REVERT: A 329 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7281 (mm-40) REVERT: A 353 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8327 (mtm180) REVERT: A 377 TYR cc_start: 0.7831 (t80) cc_final: 0.7364 (t80) REVERT: A 432 ASP cc_start: 0.7541 (p0) cc_final: 0.7332 (p0) REVERT: A 441 LYS cc_start: 0.7895 (mmpt) cc_final: 0.7270 (mptt) REVERT: A 600 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8224 (tttp) REVERT: A 691 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8492 (mmmt) REVERT: A 986 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7594 (mm110) REVERT: A 989 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.7830 (mtmt) outliers start: 23 outliers final: 13 residues processed: 107 average time/residue: 0.3053 time to fit residues: 45.7903 Evaluate side-chains 106 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 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 434 ILE Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 630 ASP 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 986 GLN Chi-restraints excluded: chain A residue 989 LYS 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 46 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 67 optimal weight: 0.0670 chunk 119 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1099 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.105471 restraints weight = 18997.780| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.91 r_work: 0.3191 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.77 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 = 0.58 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 = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12519 Z= 0.225 Angle : 0.829 39.679 17599 Z= 0.381 Chirality : 0.041 0.247 1996 Planarity : 0.005 0.041 1680 Dihedral : 24.998 178.215 3109 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.22 % Favored : 94.59 % Rotamer: Outliers : 2.31 % Allowed : 24.76 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1073 helix: 0.92 (0.23), residues: 539 sheet: -1.15 (0.51), residues: 95 loop : -1.11 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1035 HIS 0.006 0.001 HIS A 27 PHE 0.015 0.002 PHE A 298 TYR 0.019 0.002 TYR A 256 ARG 0.008 0.000 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 547) hydrogen bonds : angle 4.18409 ( 1481) metal coordination : bond 0.02011 ( 14) metal coordination : angle 2.04420 ( 8) SS BOND : bond 0.00017 ( 1) SS BOND : angle 0.88593 ( 2) covalent geometry : bond 0.00515 (12504) covalent geometry : angle 0.82795 (17589) *********************** 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 107 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8849 (mt) cc_final: 0.8513 (mt) REVERT: A 26 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8019 (mm-30) REVERT: A 329 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7218 (mm-40) REVERT: A 377 TYR cc_start: 0.7960 (t80) cc_final: 0.7422 (t80) REVERT: A 441 LYS cc_start: 0.8024 (mmpt) cc_final: 0.7334 (mptt) REVERT: A 600 LYS cc_start: 0.8704 (ttmt) cc_final: 0.8265 (tttp) REVERT: A 691 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8498 (mmmt) REVERT: A 986 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7546 (mm110) REVERT: A 989 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.7975 (mtmt) outliers start: 22 outliers final: 14 residues processed: 102 average time/residue: 0.2658 time to fit residues: 39.0742 Evaluate side-chains 100 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain A residue 286 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 434 ILE 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 986 GLN Chi-restraints excluded: chain A residue 989 LYS 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 98 optimal weight: 0.5980 chunk 11 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 3 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN A1099 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.146190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105882 restraints weight = 18942.631| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.87 r_work: 0.3191 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12519 Z= 0.212 Angle : 0.821 39.857 17599 Z= 0.375 Chirality : 0.040 0.204 1996 Planarity : 0.004 0.043 1680 Dihedral : 24.962 179.440 3109 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.94 % Favored : 94.87 % Rotamer: Outliers : 1.99 % Allowed : 24.66 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1073 helix: 0.81 (0.23), residues: 540 sheet: -1.22 (0.50), residues: 95 loop : -1.15 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 489 HIS 0.005 0.001 HIS A 27 PHE 0.013 0.002 PHE A 298 TYR 0.010 0.002 TYR A 953 ARG 0.009 0.000 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 547) hydrogen bonds : angle 4.16068 ( 1481) metal coordination : bond 0.01463 ( 14) metal coordination : angle 2.14564 ( 8) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.96833 ( 2) covalent geometry : bond 0.00484 (12504) covalent geometry : angle 0.81954 (17589) ********************** 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 101 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8856 (mt) cc_final: 0.8528 (mt) REVERT: A 26 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8006 (mm-30) REVERT: A 329 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7102 (mm-40) REVERT: A 377 TYR cc_start: 0.7981 (t80) cc_final: 0.7416 (t80) REVERT: A 441 LYS cc_start: 0.8005 (mmpt) cc_final: 0.7364 (mptt) REVERT: A 600 LYS cc_start: 0.8688 (ttmt) cc_final: 0.8233 (tttp) REVERT: A 691 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8501 (mmmt) REVERT: A 989 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.7971 (mtmt) outliers start: 19 outliers final: 12 residues processed: 95 average time/residue: 0.2735 time to fit residues: 36.9372 Evaluate side-chains 91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 132 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 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 989 LYS Chi-restraints excluded: chain A residue 1085 GLU 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: 0.9980 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 96 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN A1099 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.148976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109103 restraints weight = 18919.244| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.90 r_work: 0.3244 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 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 = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2730 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= 0.136 Angle : 0.782 39.870 17599 Z= 0.355 Chirality : 0.037 0.168 1996 Planarity : 0.004 0.039 1680 Dihedral : 24.836 179.418 3109 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.41 % Favored : 94.41 % Rotamer: Outliers : 1.57 % Allowed : 25.08 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1073 helix: 1.06 (0.23), residues: 553 sheet: -1.05 (0.51), residues: 95 loop : -1.15 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 456 HIS 0.003 0.001 HIS A1099 PHE 0.011 0.001 PHE A 298 TYR 0.008 0.001 TYR A 953 ARG 0.006 0.000 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 547) hydrogen bonds : angle 3.98612 ( 1481) metal coordination : bond 0.00338 ( 14) metal coordination : angle 1.96464 ( 8) SS BOND : bond 0.00139 ( 1) SS BOND : angle 1.10295 ( 2) covalent geometry : bond 0.00304 (12504) covalent geometry : angle 0.78054 (17589) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8969.14 seconds wall clock time: 157 minutes 10.89 seconds (9430.89 seconds total)