Starting phenix.real_space_refine on Sat Sep 12 03:34:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tre_26087/09_2026/7tre_26087.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tre_26087/09_2026/7tre_26087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tre_26087/09_2026/7tre_26087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tre_26087/09_2026/7tre_26087.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tre_26087/09_2026/7tre_26087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tre_26087/09_2026/7tre_26087.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tre_26087/09_2026/7tre_26087.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tre_26087/09_2026/7tre_26087.cif" } resolution = 3.5 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 224 5.49 5 S 40 5.16 5 C 7660 2.51 5 N 2426 2.21 5 O 3061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13411 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 4605 Classifications: {'RNAv2': 217} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 20, 'rna3p_pur': 86, 'rna3p_pyr': 97} Link IDs: {'rna2p': 34, 'rna3p': 182} Chain breaks: 2 Chain: "A" Number of atoms: 7488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 934, 7488 Classifications: {'peptide': 934} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 877} Chain breaks: 4 Chain: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "C" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1171 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Time building chain proxies: 2.49, per 1000 atoms: 0.19 Number of scatterers: 13411 At special positions: 0 Unit cell: (140.8, 122.1, 108.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 224 15.00 O 3061 8.00 N 2426 7.00 C 7660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 441.8 milliseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2044 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 50.6% alpha, 14.7% beta 61 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 76 through 92 Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.542A pdb=" N PHE A 99 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.512A pdb=" N GLY A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.812A pdb=" N LEU A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 353 through 366 removed outlier: 3.730A pdb=" N ALA A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 389 through 402 removed outlier: 3.943A pdb=" N PHE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.828A pdb=" N LEU A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 453 Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.628A pdb=" N GLU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.648A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 551 removed outlier: 3.908A pdb=" N HIS A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.849A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 4.355A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 610 Processing helix chain 'A' and resid 652 through 672 removed outlier: 3.664A pdb=" N ARG A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.836A pdb=" N LEU A 676 " --> pdb=" O PRO A 673 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 677 " --> pdb=" O GLY A 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 677' Processing helix chain 'A' and resid 682 through 699 removed outlier: 3.876A pdb=" N ILE A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 699 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 Processing helix chain 'A' and resid 772 through 784 Processing helix chain 'A' and resid 802 through 814 Processing helix chain 'A' and resid 837 through 854 Processing helix chain 'A' and resid 856 through 860 removed outlier: 4.160A pdb=" N ASP A 860 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 890 removed outlier: 3.605A pdb=" N GLY A 890 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 950 removed outlier: 3.809A pdb=" N ALA A 950 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 958 removed outlier: 4.033A pdb=" N LEU A 958 " --> pdb=" O ARG A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 982 Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 993 through 1017 Processing helix chain 'A' and resid 1024 through 1027 Processing helix chain 'A' and resid 1028 through 1051 removed outlier: 4.094A pdb=" N PHE A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1082 removed outlier: 4.072A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.675A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Proline residue: A1091 - end of helix removed outlier: 4.638A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A1106 " --> pdb=" O GLN A1102 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A1107 " --> pdb=" O LEU A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1118 Processing helix chain 'C' and resid 98 through 104 removed outlier: 3.865A pdb=" N LEU C 104 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 164 Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.507A pdb=" N LYS C 170 " --> pdb=" O TRP C 167 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU C 171 " --> pdb=" O GLU C 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 167 through 171' Processing helix chain 'C' and resid 223 through 226 Processing helix chain 'C' and resid 227 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.728A pdb=" N GLU A 20 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 10.962A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 14.973A pdb=" N CYS A 171 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 20.101A pdb=" N SER A 797 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU A 798 " --> pdb=" O TYR A 739 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR A 739 " --> pdb=" O LEU A 798 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR A 744 " --> pdb=" O LYS A 760 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA4, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA5, first strand: chain 'A' and resid 598 through 600 removed outlier: 4.566A pdb=" N GLN A 827 " --> pdb=" O HIS A 816 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS A 816 " --> pdb=" O GLN A 827 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A 617 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ARG A 819 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 862 through 865 removed outlier: 3.537A pdb=" N VAL A 904 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP A 712 " --> pdb=" O LYS A 902 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS A 902 " --> pdb=" O ASP A 712 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 927 through 930 Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 120 removed outlier: 7.126A pdb=" N LEU C 145 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL C 120 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR C 143 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N LEU C 204 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG C 154 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL C 206 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU C 156 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ARG C 208 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP C 186 " --> pdb=" O ASP C 207 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE C 209 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU C 184 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU C 211 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU C 182 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ARG C 180 " --> pdb=" O PRO C 213 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG C 180 " --> pdb=" O LEU C 117 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 166 hydrogen bonds 316 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2319 1.33 - 1.45: 4595 1.45 - 1.57: 6752 1.57 - 1.69: 444 1.69 - 1.81: 51 Bond restraints: 14161 Sorted by residual: bond pdb=" C3' DG D 18 " pdb=" O3' DG D 18 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.26e+01 bond pdb=" C3' DT D 13 " pdb=" C2' DT D 13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DA D 15 " pdb=" O3' DA D 15 " ideal model delta sigma weight residual 1.435 1.399 0.036 1.30e-02 5.92e+03 7.73e+00 bond pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.41e+00 bond pdb=" C4' DG D 18 " pdb=" C3' DG D 18 " ideal model delta sigma weight residual 1.529 1.502 0.027 1.00e-02 1.00e+04 7.36e+00 ... (remaining 14156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 18840 1.73 - 3.47: 1175 3.47 - 5.20: 225 5.20 - 6.93: 21 6.93 - 8.66: 5 Bond angle restraints: 20266 Sorted by residual: angle pdb=" O4' DG D 18 " pdb=" C4' DG D 18 " pdb=" C3' DG D 18 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.78e+01 angle pdb=" N3 DT D 14 " pdb=" C4 DT D 14 " pdb=" O4 DT D 14 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT D 13 " pdb=" C4 DT D 13 " pdb=" O4 DT D 13 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 angle pdb=" N3 DT D 12 " pdb=" C4 DT D 12 " pdb=" O4 DT D 12 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 angle pdb=" C3' G B 71 " pdb=" O3' G B 71 " pdb=" P C B 72 " ideal model delta sigma weight residual 119.70 124.24 -4.54 1.20e+00 6.94e-01 1.43e+01 ... (remaining 20261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.59: 6987 23.59 - 47.18: 711 47.18 - 70.78: 294 70.78 - 94.37: 32 94.37 - 117.96: 1 Dihedral angle restraints: 8025 sinusoidal: 4871 harmonic: 3154 Sorted by residual: dihedral pdb=" C4' A B 281 " pdb=" C3' A B 281 " pdb=" C2' A B 281 " pdb=" C1' A B 281 " ideal model delta sinusoidal sigma weight residual 36.34 -39.24 75.59 1 3.10e+00 1.04e-01 7.50e+02 dihedral pdb=" C4' A B 48 " pdb=" C3' A B 48 " pdb=" C2' A B 48 " pdb=" C1' A B 48 " ideal model delta sinusoidal sigma weight residual 36.34 -38.56 74.91 1 3.10e+00 1.04e-01 7.39e+02 dihedral pdb=" C4' A B 301 " pdb=" C3' A B 301 " pdb=" C2' A B 301 " pdb=" C1' A B 301 " ideal model delta sinusoidal sigma weight residual 36.35 -37.95 74.30 1 3.10e+00 1.04e-01 7.29e+02 ... (remaining 8022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2091 0.102 - 0.203: 142 0.203 - 0.305: 230 0.305 - 0.407: 2 0.407 - 0.508: 4 Chirality restraints: 2469 Sorted by residual: chirality pdb=" P G B 63 " pdb=" OP1 G B 63 " pdb=" OP2 G B 63 " pdb=" O5' G B 63 " both_signs ideal model delta sigma weight residual True 2.17 -2.68 -0.51 2.00e-01 2.50e+01 6.46e+00 chirality pdb=" P G B 136 " pdb=" OP1 G B 136 " pdb=" OP2 G B 136 " pdb=" O5' G B 136 " both_signs ideal model delta sigma weight residual True 2.17 -2.64 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" P G B 58 " pdb=" OP1 G B 58 " pdb=" OP2 G B 58 " pdb=" O5' G B 58 " both_signs ideal model delta sigma weight residual True 2.17 -2.64 -0.47 2.00e-01 2.50e+01 5.52e+00 ... (remaining 2466 not shown) Planarity restraints: 1759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 216 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO C 217 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 217 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 217 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 167 " 0.027 2.00e-02 2.50e+03 1.26e-02 4.35e+00 pdb=" N9 A B 167 " -0.030 2.00e-02 2.50e+03 pdb=" C8 A B 167 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A B 167 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A B 167 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A B 167 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A B 167 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A B 167 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A B 167 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 167 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A B 167 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 310 " 0.027 2.00e-02 2.50e+03 1.19e-02 4.23e+00 pdb=" N9 G B 310 " -0.029 2.00e-02 2.50e+03 pdb=" C8 G B 310 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G B 310 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 310 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B 310 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G B 310 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G B 310 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B 310 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 310 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G B 310 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B 310 " -0.004 2.00e-02 2.50e+03 ... (remaining 1756 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1175 2.73 - 3.27: 12061 3.27 - 3.82: 22665 3.82 - 4.36: 26991 4.36 - 4.90: 41781 Nonbonded interactions: 104673 Sorted by model distance: nonbonded pdb=" O2' A B 175 " pdb=" OP1 A B 176 " model vdw 2.188 3.040 nonbonded pdb=" O LEU A1079 " pdb=" OG1 THR A1083 " model vdw 2.200 3.040 nonbonded pdb=" O2' U B 314 " pdb=" OE2 GLU A 538 " model vdw 2.203 3.040 nonbonded pdb=" O2' A B 48 " pdb=" OP2 A B 49 " model vdw 2.251 3.040 nonbonded pdb=" N1 G B 93 " pdb=" O6 G B 121 " model vdw 2.253 3.120 ... (remaining 104668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.110 Find NCS groups from input model: 0.040 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14161 Z= 0.303 Angle : 0.939 8.664 20266 Z= 0.451 Chirality : 0.094 0.508 2469 Planarity : 0.005 0.054 1759 Dihedral : 19.642 117.962 5981 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.11 % Allowed : 0.64 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.25), residues: 1074 helix: 0.82 (0.24), residues: 477 sheet: -1.09 (0.38), residues: 131 loop : -1.73 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1011 TYR 0.018 0.002 TYR A 122 PHE 0.026 0.003 PHE A 331 TRP 0.028 0.002 TRP C 167 HIS 0.008 0.002 HIS A 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.30 (14161) covalent geometry : angle 0.93869 / 0.45 (20266) hydrogen bonds : bond 0.12603 / 6.62 ( 576) hydrogen bonds : angle 5.11481 / 2.11 ( 1489) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 769 LEU cc_start: 0.7756 (pt) cc_final: 0.7493 (pt) REVERT: A 849 MET cc_start: 0.8015 (ttp) cc_final: 0.7571 (ttp) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.1607 time to fit residues: 38.8968 Evaluate side-chains 80 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 748 GLN A 779 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.145587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.093606 restraints weight = 27775.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.096337 restraints weight = 14220.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.097894 restraints weight = 10236.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.098771 restraints weight = 8765.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.098977 restraints weight = 8123.644| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14161 Z= 0.227 Angle : 1.340 21.661 20266 Z= 0.534 Chirality : 0.116 1.359 2469 Planarity : 0.006 0.052 1759 Dihedral : 18.287 142.920 3882 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.85 % Allowed : 8.94 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.26), residues: 1074 helix: 1.25 (0.24), residues: 478 sheet: -0.86 (0.39), residues: 135 loop : -1.45 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 113 TYR 0.010 0.001 TYR A 946 PHE 0.019 0.002 PHE A 331 TRP 0.035 0.002 TRP A 60 HIS 0.010 0.001 HIS A 925 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.23 (14161) covalent geometry : angle 1.34004 / 0.53 (20266) hydrogen bonds : bond 0.05243 / 2.83 ( 576) hydrogen bonds : angle 4.39555 / 1.79 ( 1489) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 849 MET cc_start: 0.8681 (ttp) cc_final: 0.8271 (ttp) REVERT: A 1054 MET cc_start: 0.7675 (tpp) cc_final: 0.7140 (ttt) outliers start: 8 outliers final: 5 residues processed: 96 average time/residue: 0.1140 time to fit residues: 16.1313 Evaluate side-chains 75 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1090 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN A 384 GLN A 635 ASN A 770 GLN A 779 HIS ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.140265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.086666 restraints weight = 27998.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.089216 restraints weight = 14939.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.090714 restraints weight = 11027.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.091435 restraints weight = 9533.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.091868 restraints weight = 8910.469| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14161 Z= 0.275 Angle : 1.053 13.433 20266 Z= 0.440 Chirality : 0.076 0.597 2469 Planarity : 0.006 0.047 1759 Dihedral : 18.445 157.342 3882 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.91 % Allowed : 12.13 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.25), residues: 1074 helix: 1.03 (0.24), residues: 484 sheet: -0.97 (0.39), residues: 130 loop : -1.43 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 938 TYR 0.024 0.002 TYR A 176 PHE 0.028 0.002 PHE A 331 TRP 0.065 0.004 TRP A 60 HIS 0.027 0.003 HIS A 925 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.27 (14161) covalent geometry : angle 1.05303 / 0.44 (20266) hydrogen bonds : bond 0.06009 / 3.18 ( 576) hydrogen bonds : angle 4.38444 / 1.80 ( 1489) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 78 LYS cc_start: 0.8442 (mtpp) cc_final: 0.7948 (tmtt) REVERT: A 85 LEU cc_start: 0.9249 (mt) cc_final: 0.9031 (pp) REVERT: A 794 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7690 (mm110) REVERT: A 807 ASP cc_start: 0.8472 (t0) cc_final: 0.8130 (t0) REVERT: A 811 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8236 (mpp80) REVERT: A 849 MET cc_start: 0.8707 (ttp) cc_final: 0.8481 (ttp) REVERT: A 1054 MET cc_start: 0.7662 (tpp) cc_final: 0.7205 (ttt) REVERT: C 122 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7042 (tt0) outliers start: 18 outliers final: 10 residues processed: 85 average time/residue: 0.1256 time to fit residues: 15.2901 Evaluate side-chains 75 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain C residue 158 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 117 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN A 779 HIS ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.140325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.086805 restraints weight = 27797.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.089359 restraints weight = 14791.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.090871 restraints weight = 10897.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.091677 restraints weight = 9418.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.091898 restraints weight = 8791.548| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14161 Z= 0.209 Angle : 0.953 13.072 20266 Z= 0.396 Chirality : 0.070 0.569 2469 Planarity : 0.005 0.043 1759 Dihedral : 18.141 151.446 3882 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.02 % Allowed : 13.40 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.26), residues: 1074 helix: 1.09 (0.24), residues: 485 sheet: -0.90 (0.40), residues: 123 loop : -1.34 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 132 TYR 0.009 0.001 TYR A 176 PHE 0.023 0.002 PHE A 47 TRP 0.038 0.002 TRP A 60 HIS 0.007 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (14161) covalent geometry : angle 0.95261 / 0.40 (20266) hydrogen bonds : bond 0.05140 / 2.74 ( 576) hydrogen bonds : angle 4.22516 / 1.74 ( 1489) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9247 (mt) cc_final: 0.9020 (pp) REVERT: A 849 MET cc_start: 0.8616 (ttp) cc_final: 0.8379 (ttp) REVERT: A 1023 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: A 1054 MET cc_start: 0.7530 (tpp) cc_final: 0.7280 (ttt) REVERT: C 122 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7124 (tt0) outliers start: 19 outliers final: 14 residues processed: 91 average time/residue: 0.1259 time to fit residues: 16.6165 Evaluate side-chains 85 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1023 GLN Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain C residue 158 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 3 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 74 optimal weight: 0.0570 chunk 127 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS A 794 GLN ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.140330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.086904 restraints weight = 27839.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.089531 restraints weight = 14744.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.091068 restraints weight = 10823.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.091802 restraints weight = 9336.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.092180 restraints weight = 8735.220| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14161 Z= 0.174 Angle : 0.906 12.706 20266 Z= 0.374 Chirality : 0.066 0.508 2469 Planarity : 0.005 0.043 1759 Dihedral : 18.023 152.117 3882 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.13 % Allowed : 15.32 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 1074 helix: 1.33 (0.24), residues: 485 sheet: -0.57 (0.41), residues: 130 loop : -1.26 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 657 TYR 0.009 0.001 TYR A 168 PHE 0.023 0.002 PHE A 47 TRP 0.039 0.002 TRP A 60 HIS 0.023 0.002 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (14161) covalent geometry : angle 0.90607 / 0.37 (20266) hydrogen bonds : bond 0.04852 / 2.60 ( 576) hydrogen bonds : angle 4.07067 / 1.67 ( 1489) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 TRP cc_start: 0.6888 (t-100) cc_final: 0.6045 (t-100) REVERT: A 85 LEU cc_start: 0.9251 (mt) cc_final: 0.9024 (pp) REVERT: A 362 GLU cc_start: 0.8423 (tp30) cc_final: 0.8035 (tt0) REVERT: A 1023 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8497 (mt0) REVERT: A 1054 MET cc_start: 0.7489 (tpp) cc_final: 0.7270 (ttt) REVERT: C 100 ARG cc_start: 0.7991 (mmp80) cc_final: 0.7491 (mmm160) REVERT: C 122 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7145 (tt0) REVERT: C 154 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7496 (mtp85) outliers start: 20 outliers final: 15 residues processed: 95 average time/residue: 0.1409 time to fit residues: 18.7077 Evaluate side-chains 96 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1023 GLN Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 236 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 88 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.0270 chunk 18 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN A 779 HIS A1051 ASN C 151 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.142616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.090006 restraints weight = 27910.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092664 restraints weight = 14423.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.094318 restraints weight = 10484.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.095137 restraints weight = 8929.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.095469 restraints weight = 8309.055| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14161 Z= 0.123 Angle : 0.852 12.220 20266 Z= 0.350 Chirality : 0.062 0.459 2469 Planarity : 0.004 0.045 1759 Dihedral : 17.785 151.786 3882 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.34 % Allowed : 16.17 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.27), residues: 1074 helix: 1.66 (0.25), residues: 483 sheet: -0.52 (0.41), residues: 129 loop : -1.25 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 657 TYR 0.009 0.001 TYR A 168 PHE 0.027 0.001 PHE A 47 TRP 0.030 0.002 TRP C 98 HIS 0.012 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (14161) covalent geometry : angle 0.85233 / 0.35 (20266) hydrogen bonds : bond 0.04135 / 2.30 ( 576) hydrogen bonds : angle 3.88160 / 1.60 ( 1489) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7781 (ptp-110) REVERT: A 60 TRP cc_start: 0.6882 (t-100) cc_final: 0.6161 (t-100) REVERT: A 85 LEU cc_start: 0.9268 (mt) cc_final: 0.9026 (pp) REVERT: A 362 GLU cc_start: 0.8312 (tp30) cc_final: 0.7999 (tt0) REVERT: A 970 MET cc_start: 0.9216 (ttm) cc_final: 0.8994 (ttt) REVERT: A 1023 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: C 122 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7130 (tt0) REVERT: C 154 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7421 (mtp85) REVERT: C 220 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7394 (ttp80) outliers start: 22 outliers final: 13 residues processed: 100 average time/residue: 0.1451 time to fit residues: 20.2922 Evaluate side-chains 90 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 1023 GLN Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 236 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 30 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 779 HIS A 794 GLN A 816 HIS C 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.141459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.088606 restraints weight = 27758.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.091235 restraints weight = 14518.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092758 restraints weight = 10583.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093630 restraints weight = 9074.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.094057 restraints weight = 8449.445| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14161 Z= 0.142 Angle : 0.850 12.107 20266 Z= 0.348 Chirality : 0.061 0.454 2469 Planarity : 0.004 0.043 1759 Dihedral : 17.717 151.191 3882 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.70 % Allowed : 16.70 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.27), residues: 1074 helix: 1.71 (0.25), residues: 484 sheet: -0.41 (0.41), residues: 129 loop : -1.23 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 100 TYR 0.008 0.001 TYR A 168 PHE 0.026 0.001 PHE A 47 TRP 0.016 0.002 TRP A 60 HIS 0.009 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (14161) covalent geometry : angle 0.84974 / 0.35 (20266) hydrogen bonds : bond 0.04286 / 2.35 ( 576) hydrogen bonds : angle 3.91773 / 1.61 ( 1489) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8059 (ptm160) REVERT: A 60 TRP cc_start: 0.6771 (t-100) cc_final: 0.6014 (t-100) REVERT: A 85 LEU cc_start: 0.9265 (mt) cc_final: 0.9027 (pp) REVERT: A 362 GLU cc_start: 0.8321 (tp30) cc_final: 0.7953 (tt0) REVERT: A 1023 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8351 (mt0) REVERT: C 101 GLU cc_start: 0.8307 (tt0) cc_final: 0.7932 (tt0) REVERT: C 122 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7190 (tt0) REVERT: C 154 ARG cc_start: 0.8015 (mtm110) cc_final: 0.7445 (mtp85) REVERT: C 220 ARG cc_start: 0.7915 (ttp80) cc_final: 0.7427 (ttp80) outliers start: 16 outliers final: 12 residues processed: 97 average time/residue: 0.1473 time to fit residues: 19.8643 Evaluate side-chains 91 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 1023 GLN Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.0570 chunk 124 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 66 optimal weight: 0.0370 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.1980 chunk 25 optimal weight: 7.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 779 HIS A 816 HIS A 925 HIS C 151 HIS C 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.142744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.090156 restraints weight = 27505.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092828 restraints weight = 14402.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.094392 restraints weight = 10506.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.095128 restraints weight = 9008.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.095602 restraints weight = 8396.898| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14161 Z= 0.115 Angle : 0.837 12.069 20266 Z= 0.342 Chirality : 0.061 0.446 2469 Planarity : 0.004 0.044 1759 Dihedral : 17.639 150.860 3882 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.60 % Allowed : 17.23 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.27), residues: 1074 helix: 1.80 (0.25), residues: 483 sheet: -0.38 (0.41), residues: 129 loop : -1.20 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 100 TYR 0.008 0.001 TYR A 168 PHE 0.027 0.001 PHE A 47 TRP 0.015 0.001 TRP A 137 HIS 0.018 0.001 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (14161) covalent geometry : angle 0.83742 / 0.34 (20266) hydrogen bonds : bond 0.03985 / 2.20 ( 576) hydrogen bonds : angle 3.87852 / 1.59 ( 1489) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8064 (ptm160) REVERT: A 60 TRP cc_start: 0.6717 (t-100) cc_final: 0.5963 (t-100) REVERT: A 85 LEU cc_start: 0.9262 (mt) cc_final: 0.9023 (pp) REVERT: A 362 GLU cc_start: 0.8219 (tp30) cc_final: 0.7901 (tt0) REVERT: A 1023 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8258 (mt0) REVERT: C 101 GLU cc_start: 0.8301 (tt0) cc_final: 0.7943 (tt0) REVERT: C 122 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7201 (tt0) REVERT: C 154 ARG cc_start: 0.8007 (mtm110) cc_final: 0.7429 (mtp85) REVERT: C 168 GLU cc_start: 0.7538 (pm20) cc_final: 0.7246 (pm20) REVERT: C 220 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7422 (ttp80) outliers start: 15 outliers final: 8 residues processed: 93 average time/residue: 0.1592 time to fit residues: 20.1443 Evaluate side-chains 82 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 1023 GLN Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 73 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 779 HIS C 151 HIS C 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.142502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.089894 restraints weight = 27858.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.092562 restraints weight = 14520.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.094068 restraints weight = 10512.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.094997 restraints weight = 9033.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.095340 restraints weight = 8356.055| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14161 Z= 0.125 Angle : 0.826 12.012 20266 Z= 0.339 Chirality : 0.060 0.436 2469 Planarity : 0.004 0.043 1759 Dihedral : 17.531 150.929 3882 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.70 % Allowed : 16.91 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.27), residues: 1074 helix: 1.83 (0.25), residues: 484 sheet: -0.24 (0.43), residues: 129 loop : -1.18 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 100 TYR 0.007 0.001 TYR A 894 PHE 0.028 0.001 PHE A 47 TRP 0.019 0.002 TRP A 137 HIS 0.013 0.001 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (14161) covalent geometry : angle 0.82590 / 0.34 (20266) hydrogen bonds : bond 0.04057 / 2.23 ( 576) hydrogen bonds : angle 3.83701 / 1.57 ( 1489) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 TRP cc_start: 0.6818 (t-100) cc_final: 0.6118 (t-100) REVERT: A 85 LEU cc_start: 0.9258 (mt) cc_final: 0.9023 (pp) REVERT: A 362 GLU cc_start: 0.8286 (tp30) cc_final: 0.7945 (tt0) REVERT: A 712 ASP cc_start: 0.7750 (t0) cc_final: 0.7539 (t0) REVERT: A 1023 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: C 122 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7172 (tt0) REVERT: C 154 ARG cc_start: 0.8096 (mtm110) cc_final: 0.7447 (mtp85) REVERT: C 220 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7451 (ttp80) REVERT: C 239 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7576 (mp0) outliers start: 16 outliers final: 11 residues processed: 94 average time/residue: 0.1511 time to fit residues: 19.7098 Evaluate side-chains 92 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1023 GLN Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 158 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 6 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 117 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 124 optimal weight: 0.4980 chunk 77 optimal weight: 0.0980 chunk 69 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 687 HIS A 779 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.143504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.091260 restraints weight = 27772.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.093951 restraints weight = 14393.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.095547 restraints weight = 10396.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096403 restraints weight = 8892.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.096544 restraints weight = 8251.700| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14161 Z= 0.115 Angle : 0.812 11.879 20266 Z= 0.333 Chirality : 0.059 0.416 2469 Planarity : 0.004 0.044 1759 Dihedral : 17.437 152.397 3882 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.38 % Allowed : 17.13 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.27), residues: 1074 helix: 1.88 (0.25), residues: 484 sheet: -0.23 (0.43), residues: 129 loop : -1.14 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 15 TYR 0.011 0.001 TYR A 168 PHE 0.026 0.001 PHE A 47 TRP 0.018 0.002 TRP A 137 HIS 0.008 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (14161) covalent geometry : angle 0.81192 / 0.33 (20266) hydrogen bonds : bond 0.03852 / 2.14 ( 576) hydrogen bonds : angle 3.82205 / 1.56 ( 1489) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 TRP cc_start: 0.6839 (t-100) cc_final: 0.6150 (t-100) REVERT: A 85 LEU cc_start: 0.9255 (mt) cc_final: 0.9014 (pp) REVERT: A 362 GLU cc_start: 0.8206 (tp30) cc_final: 0.7910 (tt0) REVERT: A 1023 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8205 (mt0) REVERT: A 1054 MET cc_start: 0.6770 (ttt) cc_final: 0.6482 (ttt) REVERT: C 122 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7174 (tt0) REVERT: C 154 ARG cc_start: 0.8095 (mtm110) cc_final: 0.7474 (mtp85) REVERT: C 168 GLU cc_start: 0.7477 (pm20) cc_final: 0.7125 (pm20) REVERT: C 220 ARG cc_start: 0.7868 (ttp80) cc_final: 0.7412 (ttp80) REVERT: C 239 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7500 (mp0) outliers start: 13 outliers final: 11 residues processed: 88 average time/residue: 0.1353 time to fit residues: 16.6782 Evaluate side-chains 92 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 1023 GLN Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 158 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 90 optimal weight: 0.0270 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 779 HIS C 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.142203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089268 restraints weight = 28079.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.091929 restraints weight = 14746.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.093510 restraints weight = 10737.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.094364 restraints weight = 9205.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094687 restraints weight = 8567.418| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14161 Z= 0.139 Angle : 0.813 11.823 20266 Z= 0.334 Chirality : 0.059 0.413 2469 Planarity : 0.004 0.043 1759 Dihedral : 17.413 154.077 3882 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.81 % Allowed : 16.70 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.27), residues: 1074 helix: 1.85 (0.25), residues: 484 sheet: -0.26 (0.43), residues: 129 loop : -1.15 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 15 TYR 0.007 0.001 TYR A 168 PHE 0.026 0.001 PHE A 47 TRP 0.018 0.002 TRP A 137 HIS 0.030 0.002 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (14161) covalent geometry : angle 0.81254 / 0.33 (20266) hydrogen bonds : bond 0.04048 / 2.23 ( 576) hydrogen bonds : angle 3.83099 / 1.56 ( 1489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2437.13 seconds wall clock time: 42 minutes 43.71 seconds (2563.71 seconds total)