Starting phenix.real_space_refine on Wed Sep 17 22:33:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nl3_49516/09_2025/9nl3_49516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nl3_49516/09_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_49516/09_2025/9nl3_49516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nl3_49516/09_2025/9nl3_49516.map" model { file = "/net/cci-nas-00/data/ceres_data/9nl3_49516/09_2025/9nl3_49516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nl3_49516/09_2025/9nl3_49516.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 121 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 159 5.49 5 Mg 1 5.21 5 S 51 5.16 5 C 6993 2.51 5 N 2165 2.21 5 O 2566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11939 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8655 Classifications: {'peptide': 1079} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1028} Chain breaks: 2 Chain: "B" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 791 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "P" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1140 Classifications: {'RNA': 53} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 24, 'rna3p_pyr': 17} Link IDs: {'rna2p': 12, 'rna3p': 40} Chain breaks: 2 Chain: "T" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1052 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 34 Unusual residues: {' MG': 1, ' ZN': 4, 'TTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 310 SG CYS A 41 55.775 30.513 64.736 1.00 86.53 S ATOM 330 SG CYS A 44 58.211 31.927 62.111 1.00 93.20 S ATOM 465 SG CYS A 61 54.773 31.941 61.304 1.00 82.06 S ATOM 579 SG CYS A 76 76.412 46.802 52.258 1.00 97.02 S ATOM 601 SG CYS A 79 74.639 44.489 54.904 1.00 89.57 S ATOM 7222 SG CYS A 991 31.997 32.857 97.447 1.00 79.38 S ATOM 7249 SG CYS A 994 28.609 32.222 98.899 1.00 63.53 S ATOM 7348 SG CYS A1008 31.554 33.293 101.124 1.00 79.09 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' TTP A1206 " occ=0.65 ... (27 atoms not shown) pdb=" PG TTP A1206 " occ=0.65 Time building chain proxies: 2.99, per 1000 atoms: 0.25 Number of scatterers: 11939 At special positions: 0 Unit cell: (122.616, 119.472, 139.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 51 16.00 P 159 15.00 Mg 1 11.99 O 2566 8.00 N 2165 7.00 C 6993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 11 " - pdb=" SG CYS A 13 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 460.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 32 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 27 " pdb=" ZN A1202 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A 57 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 61 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 44 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 41 " pdb=" ZN A1203 " pdb="ZN ZN A1203 " - pdb=" NE2 HIS A 92 " pdb="ZN ZN A1203 " - pdb=" NE2 HIS A 97 " pdb="ZN ZN A1203 " - pdb=" SG CYS A 76 " pdb="ZN ZN A1203 " - pdb=" SG CYS A 79 " pdb=" ZN A1204 " pdb="ZN ZN A1204 " - pdb=" NE2 HIS A1003 " pdb="ZN ZN A1204 " - pdb=" SG CYS A 991 " pdb="ZN ZN A1204 " - pdb=" SG CYS A 994 " pdb="ZN ZN A1204 " - pdb=" SG CYS A1008 " Number of angles added : 8 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 56.1% alpha, 8.7% beta 55 base pairs and 99 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 50 through 58 removed outlier: 3.582A pdb=" N VAL A 54 " --> pdb=" O ASN A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 97 through 110 removed outlier: 3.749A pdb=" N GLN A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.622A pdb=" N LEU A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 157 through 171 removed outlier: 4.230A pdb=" N SER A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 267 removed outlier: 3.700A pdb=" N ALA A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.671A pdb=" N GLU A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 304 removed outlier: 5.159A pdb=" N CYS A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.876A pdb=" N ARG A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.692A pdb=" N ASP A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.844A pdb=" N LEU A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LYS A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 385 Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.587A pdb=" N ARG A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 447 through 460 removed outlier: 3.826A pdb=" N ASN A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 496 through 514 removed outlier: 3.663A pdb=" N PHE A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 547 removed outlier: 3.523A pdb=" N LEU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 565 through 576 Processing helix chain 'A' and resid 579 through 590 Processing helix chain 'A' and resid 619 through 640 removed outlier: 4.691A pdb=" N LEU A 623 " --> pdb=" O PRO A 619 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 667 through 684 Processing helix chain 'A' and resid 745 through 759 Processing helix chain 'A' and resid 763 through 775 removed outlier: 3.526A pdb=" N THR A 768 " --> pdb=" O PRO A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 786 removed outlier: 3.582A pdb=" N LEU A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR A 781 " --> pdb=" O PRO A 777 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A 782 " --> pdb=" O ARG A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 808 Processing helix chain 'A' and resid 815 through 821 removed outlier: 4.347A pdb=" N LEU A 819 " --> pdb=" O CYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 826 removed outlier: 3.832A pdb=" N GLY A 826 " --> pdb=" O THR A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 850 Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.623A pdb=" N PHE A 859 " --> pdb=" O MET A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 876 Processing helix chain 'A' and resid 919 through 931 Processing helix chain 'A' and resid 937 through 942 Processing helix chain 'A' and resid 948 through 953 removed outlier: 3.881A pdb=" N GLN A 952 " --> pdb=" O ASN A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 removed outlier: 3.665A pdb=" N THR A 964 " --> pdb=" O ARG A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 983 through 987 Processing helix chain 'A' and resid 1000 through 1007 removed outlier: 3.604A pdb=" N ILE A1005 " --> pdb=" O CYS A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1010 No H-bonds generated for 'chain 'A' and resid 1008 through 1010' Processing helix chain 'A' and resid 1011 through 1033 removed outlier: 3.531A pdb=" N LYS A1033 " --> pdb=" O GLU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1091 removed outlier: 3.651A pdb=" N GLU A1081 " --> pdb=" O SER A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 removed outlier: 3.546A pdb=" N HIS A1099 " --> pdb=" O THR A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1130 removed outlier: 3.950A pdb=" N LEU A1126 " --> pdb=" O ASP A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1168 removed outlier: 3.569A pdb=" N ASP A1154 " --> pdb=" O PHE A1150 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A1168 " --> pdb=" O ARG A1164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 removed outlier: 3.725A pdb=" N TRP A 74 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 495 removed outlier: 7.345A pdb=" N CYS A 469 " --> pdb=" O TYR A 596 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N THR A 598 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR A 471 " --> pdb=" O THR A 598 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 595 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 652 through 655 removed outlier: 3.920A pdb=" N LEU A 659 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS A 693 " --> pdb=" O PHE A 554 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 652 through 655 removed outlier: 3.920A pdb=" N LEU A 659 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS A 693 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A 694 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 643 through 644 removed outlier: 3.633A pdb=" N TYR A 643 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 713 through 714 removed outlier: 3.513A pdb=" N ILE A 714 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 717 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 728 through 730 Processing sheet with id=AA9, first strand: chain 'A' and resid 1036 through 1037 removed outlier: 6.024A pdb=" N ALA A1063 " --> pdb=" O THR A1107 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A1109 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A1065 " --> pdb=" O VAL A1109 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE A1111 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP A1067 " --> pdb=" O PHE A1111 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU A1113 " --> pdb=" O ASP A1067 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR A1069 " --> pdb=" O LEU A1113 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 99 stacking parallelities Total time for adding SS restraints: 3.58 Time building geometry restraints manager: 1.10 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.710 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.140 ------------------------------------------------------------------------------- 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 : 8.10 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.71 % Favored : 92.82 % Rotamer: Outliers : 0.63 % Allowed : 21.72 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.26), residues: 1073 helix: -0.02 (0.24), residues: 505 sheet: -2.42 (0.51), residues: 92 loop : -1.61 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 490 TYR 0.018 0.001 TYR A 256 PHE 0.013 0.001 PHE A1150 TRP 0.007 0.001 TRP A 541 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00462 (12504) covalent geometry : angle 1.05636 (17589) SS BOND : bond 0.00242 ( 1) SS BOND : angle 1.61895 ( 2) hydrogen bonds : bond 0.14131 ( 547) hydrogen bonds : angle 6.78496 ( 1481) metal coordination : bond 0.01226 ( 14) metal coordination : angle 4.89862 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 165 ARG cc_start: -0.0412 (OUTLIER) cc_final: -0.1404 (mtm-85) REVERT: A 669 MET cc_start: 0.8956 (tpp) cc_final: 0.8611 (tpp) outliers start: 6 outliers final: 3 residues processed: 87 average time/residue: 0.1297 time to fit residues: 15.8581 Evaluate side-chains 84 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 1101 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0270 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 670 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.145757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105762 restraints weight = 18822.813| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.88 r_work: 0.3192 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12519 Z= 0.236 Angle : 0.894 39.898 17599 Z= 0.415 Chirality : 0.043 0.311 1996 Planarity : 0.005 0.043 1680 Dihedral : 25.904 178.154 3118 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.31 % Favored : 94.32 % Rotamer: Outliers : 3.57 % Allowed : 21.09 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.26), residues: 1073 helix: 0.20 (0.23), residues: 535 sheet: -2.22 (0.49), residues: 95 loop : -1.44 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 490 TYR 0.017 0.002 TYR A 377 PHE 0.014 0.002 PHE A1150 TRP 0.019 0.002 TRP A 489 HIS 0.005 0.001 HIS A1019 Details of bonding type rmsd covalent geometry : bond 0.00527 (12504) covalent geometry : angle 0.89119 (17589) SS BOND : bond 0.00025 ( 1) SS BOND : angle 1.44781 ( 2) hydrogen bonds : bond 0.05515 ( 547) hydrogen bonds : angle 4.82171 ( 1481) metal coordination : bond 0.01403 ( 14) metal coordination : angle 3.20387 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 291 ASN cc_start: 0.7275 (m-40) cc_final: 0.7051 (m-40) REVERT: A 329 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.6978 (mm-40) REVERT: A 465 MET cc_start: 0.8270 (ptm) cc_final: 0.7907 (ptt) REVERT: A 550 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8638 (tp) REVERT: A 691 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8436 (mmmt) REVERT: A 989 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8072 (mtmt) outliers start: 34 outliers final: 12 residues processed: 108 average time/residue: 0.1316 time to fit residues: 19.4592 Evaluate side-chains 89 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 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 620 MET Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 112 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107384 restraints weight = 19061.775| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.90 r_work: 0.3216 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12519 Z= 0.167 Angle : 0.810 40.072 17599 Z= 0.374 Chirality : 0.039 0.250 1996 Planarity : 0.005 0.042 1680 Dihedral : 25.607 179.846 3113 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.75 % Favored : 94.97 % Rotamer: Outliers : 2.62 % Allowed : 22.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.26), residues: 1073 helix: 0.45 (0.23), residues: 534 sheet: -1.90 (0.50), residues: 93 loop : -1.34 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 956 TYR 0.011 0.001 TYR A 257 PHE 0.012 0.002 PHE A1159 TRP 0.009 0.001 TRP A 489 HIS 0.005 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00376 (12504) covalent geometry : angle 0.80865 (17589) SS BOND : bond 0.00084 ( 1) SS BOND : angle 1.21990 ( 2) hydrogen bonds : bond 0.04915 ( 547) hydrogen bonds : angle 4.57464 ( 1481) metal coordination : bond 0.00786 ( 14) metal coordination : angle 2.21198 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8124 (mp0) cc_final: 0.7777 (mp0) REVERT: A 329 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6967 (mm-40) REVERT: A 377 TYR cc_start: 0.7959 (t80) cc_final: 0.7682 (t80) REVERT: A 441 LYS cc_start: 0.8062 (mmpt) cc_final: 0.7545 (tttt) REVERT: A 465 MET cc_start: 0.8277 (ptm) cc_final: 0.7938 (ptt) REVERT: A 691 LYS cc_start: 0.8973 (mmtt) cc_final: 0.8373 (mmmt) REVERT: A 736 ASP cc_start: 0.9065 (t0) cc_final: 0.8789 (t70) outliers start: 25 outliers final: 12 residues processed: 102 average time/residue: 0.1258 time to fit residues: 18.3001 Evaluate side-chains 93 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 89 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 0.0050 chunk 114 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 0.0770 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 0.0770 chunk 83 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 overall best weight: 0.2310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN A 993 HIS A1012 GLN A1099 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.151399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112031 restraints weight = 19108.245| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.93 r_work: 0.3289 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12519 Z= 0.129 Angle : 0.783 40.053 17599 Z= 0.358 Chirality : 0.037 0.229 1996 Planarity : 0.004 0.044 1680 Dihedral : 25.250 179.951 3113 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.22 % Favored : 94.59 % Rotamer: Outliers : 2.52 % Allowed : 23.08 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.26), residues: 1073 helix: 0.84 (0.23), residues: 539 sheet: -1.59 (0.50), residues: 95 loop : -1.26 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 490 TYR 0.011 0.001 TYR A 257 PHE 0.026 0.001 PHE A 139 TRP 0.007 0.001 TRP A 124 HIS 0.010 0.001 HIS A1099 Details of bonding type rmsd covalent geometry : bond 0.00284 (12504) covalent geometry : angle 0.78158 (17589) SS BOND : bond 0.00160 ( 1) SS BOND : angle 1.29742 ( 2) hydrogen bonds : bond 0.04290 ( 547) hydrogen bonds : angle 4.15248 ( 1481) metal coordination : bond 0.00513 ( 14) metal coordination : angle 1.98873 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8057 (mm-30) REVERT: A 353 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8350 (mtm180) REVERT: A 377 TYR cc_start: 0.7952 (t80) cc_final: 0.7625 (t80) REVERT: A 432 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7245 (p0) REVERT: A 441 LYS cc_start: 0.7986 (mmpt) cc_final: 0.7130 (mptt) REVERT: A 465 MET cc_start: 0.8193 (ptm) cc_final: 0.7882 (ptt) REVERT: A 490 ARG cc_start: 0.6232 (ttt90) cc_final: 0.5977 (ttt180) REVERT: A 550 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8633 (tp) REVERT: A 600 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8218 (tttp) REVERT: A 691 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8483 (mmmt) REVERT: A 704 TYR cc_start: 0.8741 (p90) cc_final: 0.8479 (p90) REVERT: A 736 ASP cc_start: 0.8978 (t0) cc_final: 0.8720 (t70) outliers start: 24 outliers final: 9 residues processed: 110 average time/residue: 0.1181 time to fit residues: 18.5778 Evaluate side-chains 94 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 48 optimal weight: 0.0870 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.147761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107438 restraints weight = 18999.592| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.91 r_work: 0.3216 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12519 Z= 0.180 Angle : 0.800 39.964 17599 Z= 0.366 Chirality : 0.039 0.233 1996 Planarity : 0.005 0.046 1680 Dihedral : 25.174 178.181 3111 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.38 % Favored : 95.34 % Rotamer: Outliers : 3.04 % Allowed : 24.24 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.26), residues: 1073 helix: 0.78 (0.23), residues: 542 sheet: -1.48 (0.50), residues: 97 loop : -1.21 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1062 TYR 0.011 0.001 TYR A 953 PHE 0.011 0.002 PHE A1150 TRP 0.009 0.001 TRP A1035 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00412 (12504) covalent geometry : angle 0.79953 (17589) SS BOND : bond 0.00059 ( 1) SS BOND : angle 1.02859 ( 2) hydrogen bonds : bond 0.04416 ( 547) hydrogen bonds : angle 4.20134 ( 1481) metal coordination : bond 0.01229 ( 14) metal coordination : angle 1.76023 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8879 (mt) cc_final: 0.8585 (mt) REVERT: A 26 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8047 (mm-30) REVERT: A 329 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7026 (mm-40) REVERT: A 353 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8277 (mtm180) REVERT: A 377 TYR cc_start: 0.8034 (t80) cc_final: 0.7577 (t80) REVERT: A 441 LYS cc_start: 0.7908 (mmpt) cc_final: 0.7237 (mptt) REVERT: A 669 MET cc_start: 0.8840 (tpp) cc_final: 0.8625 (tpp) REVERT: A 691 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8475 (mmmt) REVERT: A 736 ASP cc_start: 0.9072 (t0) cc_final: 0.8845 (t70) REVERT: A 989 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7907 (mtmt) outliers start: 29 outliers final: 17 residues processed: 104 average time/residue: 0.1369 time to fit residues: 19.8799 Evaluate side-chains 102 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 507 THR Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 620 MET 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 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 89 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.148205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108151 restraints weight = 18906.641| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.90 r_work: 0.3227 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.74 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 = 0.57 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 = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12519 Z= 0.158 Angle : 0.785 40.024 17599 Z= 0.357 Chirality : 0.038 0.212 1996 Planarity : 0.004 0.044 1680 Dihedral : 25.130 179.136 3111 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.75 % Favored : 95.06 % Rotamer: Outliers : 2.94 % Allowed : 24.03 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.26), residues: 1073 helix: 0.86 (0.23), residues: 548 sheet: -1.44 (0.50), residues: 97 loop : -1.19 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 490 TYR 0.011 0.001 TYR A 953 PHE 0.010 0.001 PHE A1159 TRP 0.007 0.001 TRP A1035 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00358 (12504) covalent geometry : angle 0.78454 (17589) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.96770 ( 2) hydrogen bonds : bond 0.04200 ( 547) hydrogen bonds : angle 4.14630 ( 1481) metal coordination : bond 0.00775 ( 14) metal coordination : angle 1.81911 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8846 (mt) cc_final: 0.8561 (mt) REVERT: A 26 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8024 (mm-30) REVERT: A 329 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7047 (mm-40) REVERT: A 353 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8396 (mtm180) REVERT: A 377 TYR cc_start: 0.8018 (t80) cc_final: 0.7501 (t80) REVERT: A 441 LYS cc_start: 0.7948 (mmpt) cc_final: 0.7288 (mptt) REVERT: A 465 MET cc_start: 0.8348 (ptm) cc_final: 0.8055 (ptt) REVERT: A 490 ARG cc_start: 0.6384 (ttt90) cc_final: 0.6167 (ttt180) REVERT: A 691 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8495 (mmmt) REVERT: A 736 ASP cc_start: 0.9011 (t0) cc_final: 0.8775 (t70) REVERT: A 743 ARG cc_start: 0.7096 (mtm-85) cc_final: 0.6896 (mtm-85) outliers start: 28 outliers final: 21 residues processed: 100 average time/residue: 0.1276 time to fit residues: 18.0662 Evaluate side-chains 102 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 620 MET 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 946 ILE Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 30.0000 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 0.0770 chunk 117 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.148646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108707 restraints weight = 18789.770| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.91 r_work: 0.3238 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 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 = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2391 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= 0.146 Angle : 0.778 40.009 17599 Z= 0.353 Chirality : 0.037 0.202 1996 Planarity : 0.004 0.045 1680 Dihedral : 25.068 179.418 3111 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.85 % Favored : 94.97 % Rotamer: Outliers : 2.94 % Allowed : 24.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.26), residues: 1073 helix: 1.02 (0.23), residues: 551 sheet: -1.39 (0.50), residues: 97 loop : -1.19 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 490 TYR 0.010 0.001 TYR A 953 PHE 0.014 0.001 PHE A 298 TRP 0.006 0.001 TRP A1035 HIS 0.003 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00331 (12504) covalent geometry : angle 0.77678 (17589) SS BOND : bond 0.00115 ( 1) SS BOND : angle 1.04319 ( 2) hydrogen bonds : bond 0.04049 ( 547) hydrogen bonds : angle 4.05720 ( 1481) metal coordination : bond 0.00640 ( 14) metal coordination : angle 1.71810 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8841 (mt) cc_final: 0.8556 (mt) REVERT: A 26 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8004 (mm-30) REVERT: A 329 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7290 (mm-40) REVERT: A 353 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8315 (mtm180) REVERT: A 377 TYR cc_start: 0.7992 (t80) cc_final: 0.7415 (t80) REVERT: A 441 LYS cc_start: 0.7944 (mmpt) cc_final: 0.7276 (mptt) REVERT: A 490 ARG cc_start: 0.6352 (ttt90) cc_final: 0.6136 (ttt180) REVERT: A 691 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8499 (mmmt) REVERT: A 736 ASP cc_start: 0.9007 (t0) cc_final: 0.8776 (t70) REVERT: A 856 MET cc_start: 0.8485 (tmm) cc_final: 0.8261 (tmm) REVERT: A 989 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.7865 (mtmt) outliers start: 28 outliers final: 18 residues processed: 104 average time/residue: 0.1250 time to fit residues: 18.3047 Evaluate side-chains 101 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 620 MET 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 946 ILE 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 87 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.148189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108323 restraints weight = 18891.347| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.90 r_work: 0.3228 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12519 Z= 0.154 Angle : 0.784 39.992 17599 Z= 0.356 Chirality : 0.038 0.194 1996 Planarity : 0.004 0.044 1680 Dihedral : 24.988 179.413 3109 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.57 % Favored : 95.25 % Rotamer: Outliers : 3.15 % Allowed : 24.24 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.26), residues: 1073 helix: 1.06 (0.23), residues: 551 sheet: -1.13 (0.51), residues: 93 loop : -1.23 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1062 TYR 0.011 0.001 TYR A 953 PHE 0.014 0.001 PHE A 298 TRP 0.008 0.001 TRP A1035 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00351 (12504) covalent geometry : angle 0.78365 (17589) SS BOND : bond 0.00085 ( 1) SS BOND : angle 1.00689 ( 2) hydrogen bonds : bond 0.03998 ( 547) hydrogen bonds : angle 4.03444 ( 1481) metal coordination : bond 0.00757 ( 14) metal coordination : angle 1.76518 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8830 (mt) cc_final: 0.8530 (mt) REVERT: A 26 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7995 (mm-30) REVERT: A 329 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7315 (mm-40) REVERT: A 353 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8327 (mtm180) REVERT: A 377 TYR cc_start: 0.7970 (t80) cc_final: 0.7284 (t80) REVERT: A 441 LYS cc_start: 0.7938 (mmpt) cc_final: 0.7275 (mptt) REVERT: A 691 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8509 (mmmt) REVERT: A 736 ASP cc_start: 0.9016 (t0) cc_final: 0.8781 (t70) REVERT: A 989 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7858 (mtmt) outliers start: 30 outliers final: 17 residues processed: 105 average time/residue: 0.1177 time to fit residues: 17.9738 Evaluate side-chains 101 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 620 MET 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 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 80 optimal weight: 0.0270 chunk 95 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 94 optimal weight: 0.0870 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.150995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111648 restraints weight = 19085.299| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.89 r_work: 0.3281 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12519 Z= 0.123 Angle : 0.768 39.951 17599 Z= 0.347 Chirality : 0.037 0.183 1996 Planarity : 0.004 0.043 1680 Dihedral : 24.837 179.246 3109 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.66 % Favored : 95.15 % Rotamer: Outliers : 2.10 % Allowed : 25.18 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.27), residues: 1073 helix: 1.21 (0.23), residues: 551 sheet: -0.99 (0.51), residues: 93 loop : -1.14 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 490 TYR 0.010 0.001 TYR A 953 PHE 0.020 0.001 PHE A 298 TRP 0.008 0.001 TRP A 873 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00279 (12504) covalent geometry : angle 0.76723 (17589) SS BOND : bond 0.00131 ( 1) SS BOND : angle 1.13128 ( 2) hydrogen bonds : bond 0.03799 ( 547) hydrogen bonds : angle 3.88980 ( 1481) metal coordination : bond 0.00299 ( 14) metal coordination : angle 1.74548 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7989 (mm-30) REVERT: A 353 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8398 (mtm180) REVERT: A 377 TYR cc_start: 0.7939 (t80) cc_final: 0.7272 (t80) REVERT: A 441 LYS cc_start: 0.7868 (mmpt) cc_final: 0.7228 (mptt) REVERT: A 691 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8511 (mmmt) REVERT: A 736 ASP cc_start: 0.8965 (t0) cc_final: 0.8714 (t70) REVERT: A 856 MET cc_start: 0.8413 (tmm) cc_final: 0.8186 (tmm) REVERT: A 989 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7799 (mtmt) REVERT: A 1090 TYR cc_start: 0.7721 (m-10) cc_final: 0.7115 (m-80) outliers start: 20 outliers final: 12 residues processed: 105 average time/residue: 0.1213 time to fit residues: 17.8799 Evaluate side-chains 96 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG 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 860 MET Chi-restraints excluded: chain A residue 989 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 31 optimal weight: 0.0040 chunk 60 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 97 optimal weight: 0.0470 chunk 74 optimal weight: 0.8980 overall best weight: 0.7692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.149963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.110242 restraints weight = 19080.693| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.90 r_work: 0.3259 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 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 = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2811 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= 0.139 Angle : 0.780 39.939 17599 Z= 0.353 Chirality : 0.037 0.184 1996 Planarity : 0.004 0.043 1680 Dihedral : 24.798 179.949 3109 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.43 % Rotamer: Outliers : 1.78 % Allowed : 25.50 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.26), residues: 1073 helix: 1.26 (0.23), residues: 549 sheet: -0.92 (0.52), residues: 93 loop : -1.14 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 490 TYR 0.010 0.001 TYR A 953 PHE 0.012 0.001 PHE A 298 TRP 0.008 0.001 TRP A 331 HIS 0.003 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00316 (12504) covalent geometry : angle 0.77905 (17589) SS BOND : bond 0.00125 ( 1) SS BOND : angle 1.11100 ( 2) hydrogen bonds : bond 0.03799 ( 547) hydrogen bonds : angle 3.90254 ( 1481) metal coordination : bond 0.00520 ( 14) metal coordination : angle 1.62434 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.381 Fit side-chains REVERT: A 22 LEU cc_start: 0.8776 (mt) cc_final: 0.8372 (mt) REVERT: A 26 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7989 (mm-30) REVERT: A 292 GLN cc_start: 0.7395 (tp40) cc_final: 0.6893 (tp40) REVERT: A 353 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8452 (mtm180) REVERT: A 377 TYR cc_start: 0.7980 (t80) cc_final: 0.7378 (t80) REVERT: A 441 LYS cc_start: 0.7867 (mmpt) cc_final: 0.7184 (mptt) REVERT: A 691 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8517 (mmmt) REVERT: A 736 ASP cc_start: 0.8987 (t0) cc_final: 0.8749 (t70) REVERT: A 989 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7814 (mtmt) outliers start: 17 outliers final: 12 residues processed: 98 average time/residue: 0.1173 time to fit residues: 16.3382 Evaluate side-chains 99 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 167 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 604 HIS Chi-restraints excluded: chain A residue 608 ILE 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 989 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 22 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 0.0030 chunk 85 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 74 optimal weight: 0.0170 chunk 57 optimal weight: 0.9980 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.149846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109971 restraints weight = 19084.312| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.90 r_work: 0.3256 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2865 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= 0.139 Angle : 0.778 39.919 17599 Z= 0.352 Chirality : 0.038 0.185 1996 Planarity : 0.004 0.043 1680 Dihedral : 24.727 179.867 3109 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.85 % Favored : 94.97 % Rotamer: Outliers : 2.10 % Allowed : 25.39 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.26), residues: 1073 helix: 1.27 (0.23), residues: 550 sheet: -0.91 (0.51), residues: 93 loop : -1.12 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 490 TYR 0.010 0.001 TYR A 953 PHE 0.009 0.001 PHE A 298 TRP 0.008 0.001 TRP A 331 HIS 0.003 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00316 (12504) covalent geometry : angle 0.77742 (17589) SS BOND : bond 0.00119 ( 1) SS BOND : angle 1.09686 ( 2) hydrogen bonds : bond 0.03774 ( 547) hydrogen bonds : angle 3.90473 ( 1481) metal coordination : bond 0.00553 ( 14) metal coordination : angle 1.65114 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4261.38 seconds wall clock time: 73 minutes 17.41 seconds (4397.41 seconds total)