Starting phenix.real_space_refine on Thu Jul 2 04:05:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pd0_17597/07_2026/8pd0_17597.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pd0_17597/07_2026/8pd0_17597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8pd0_17597/07_2026/8pd0_17597.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pd0_17597/07_2026/8pd0_17597.cif" model { file = "/net/cci-nas-00/data/ceres_data/8pd0_17597/07_2026/8pd0_17597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pd0_17597/07_2026/8pd0_17597.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pd0_17597/07_2026/8pd0_17597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pd0_17597/07_2026/8pd0_17597.map" } resolution = 3.58 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= 0.008 sd= 0.089 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 4 5.49 5 S 29 5.16 5 C 4137 2.51 5 N 1017 2.21 5 O 1087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 6101 Classifications: {'peptide': 880} Incomplete info: {'truncation_to_alanine': 298} Link IDs: {'PTRANS': 31, 'TRANS': 848} Chain breaks: 11 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1171 Unresolved non-hydrogen angles: 1506 Unresolved non-hydrogen dihedrals: 1012 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'PHE:plan': 27, 'GLU:plan': 21, 'ARG:plan': 14, 'GLN:plan1': 8, 'TYR:plan': 16, 'ASP:plan': 14, 'HIS:plan': 7, 'ASN:plan1': 14, 'TRP:plan': 8} Unresolved non-hydrogen planarities: 651 Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 173 Unusual residues: {'PCW': 3, 'PX6': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 1.09, per 1000 atoms: 0.17 Number of scatterers: 6274 At special positions: 0 Unit cell: (82.5664, 97.888, 137.043, 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 29 16.00 P 4 15.00 O 1087 8.00 N 1017 7.00 C 4137 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: 0.44 Conformation dependent library (CDL) restraints added in 321.9 milliseconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1674 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 1 sheets defined 80.1% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 112 through 162 Proline residue: A 146 - end of helix Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.637A pdb=" N ILE A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 176' Processing helix chain 'A' and resid 187 through 226 removed outlier: 3.933A pdb=" N GLN A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLN A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 226 " --> pdb=" O MET A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 Processing helix chain 'A' and resid 469 through 525 removed outlier: 3.574A pdb=" N PHE A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 477 " --> pdb=" O ILE A 473 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA A 479 " --> pdb=" O TYR A 475 " (cutoff:3.500A) Proline residue: A 494 - end of helix removed outlier: 3.918A pdb=" N GLY A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 535 removed outlier: 4.046A pdb=" N LYS A 534 " --> pdb=" O ASN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 563 removed outlier: 3.566A pdb=" N ILE A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 553 " --> pdb=" O HIS A 549 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 597 Proline residue: A 576 - end of helix Processing helix chain 'A' and resid 607 through 655 removed outlier: 3.706A pdb=" N LEU A 612 " --> pdb=" O PRO A 608 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE A 637 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Proline residue: A 638 - end of helix removed outlier: 5.094A pdb=" N CYS A 651 " --> pdb=" O PHE A 647 " (cutoff:3.500A) Proline residue: A 652 - end of helix Processing helix chain 'A' and resid 662 through 667 removed outlier: 3.667A pdb=" N ILE A 666 " --> pdb=" O TRP A 662 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS A 667 " --> pdb=" O VAL A 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 662 through 667' Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 673 through 700 removed outlier: 3.804A pdb=" N VAL A 677 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A 699 " --> pdb=" O MET A 695 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 726 removed outlier: 3.606A pdb=" N LEU A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 725 " --> pdb=" O HIS A 721 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 720 through 726' Processing helix chain 'A' and resid 727 through 756 removed outlier: 4.029A pdb=" N GLN A 731 " --> pdb=" O PRO A 727 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 756 " --> pdb=" O PHE A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 774 Processing helix chain 'A' and resid 780 through 799 removed outlier: 3.681A pdb=" N ASN A 784 " --> pdb=" O SER A 780 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 786 " --> pdb=" O LYS A 782 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 799 " --> pdb=" O ARG A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 822 removed outlier: 3.628A pdb=" N LYS A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 829 removed outlier: 4.006A pdb=" N ILE A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 829 " --> pdb=" O SER A 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 824 through 829' Processing helix chain 'A' and resid 833 through 837 Processing helix chain 'A' and resid 844 through 851 Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'A' and resid 868 through 879 Processing helix chain 'A' and resid 905 through 909 Processing helix chain 'A' and resid 925 through 937 removed outlier: 3.605A pdb=" N GLY A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 943 removed outlier: 3.711A pdb=" N LEU A 942 " --> pdb=" O PHE A 939 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 943 " --> pdb=" O GLY A 940 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 939 through 943' Processing helix chain 'A' and resid 963 through 998 removed outlier: 3.666A pdb=" N LEU A 968 " --> pdb=" O ARG A 964 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU A 969 " --> pdb=" O TYR A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1007 removed outlier: 3.766A pdb=" N VAL A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1024 removed outlier: 3.819A pdb=" N SER A1024 " --> pdb=" O LEU A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1051 Processing helix chain 'A' and resid 1094 through 1106 removed outlier: 4.560A pdb=" N MET A1098 " --> pdb=" O GLN A1094 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A1103 " --> pdb=" O ALA A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1147 removed outlier: 3.659A pdb=" N ALA A1119 " --> pdb=" O MET A1115 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A1140 " --> pdb=" O ASP A1136 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS A1141 " --> pdb=" O GLY A1137 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR A1142 " --> pdb=" O ILE A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1162 removed outlier: 3.684A pdb=" N TRP A1162 " --> pdb=" O GLY A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1195 removed outlier: 4.079A pdb=" N LEU A1169 " --> pdb=" O TYR A1165 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU A1170 " --> pdb=" O ASP A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1234 Proline residue: A1225 - end of helix Processing helix chain 'A' and resid 1248 through 1256 Processing helix chain 'A' and resid 1267 through 1304 Processing sheet with id=AA1, first strand: chain 'A' and resid 891 through 896 removed outlier: 3.823A pdb=" N VAL A 891 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 895 " --> pdb=" O TYR A 953 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.67 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1001 1.32 - 1.44: 1670 1.44 - 1.57: 3669 1.57 - 1.69: 7 1.69 - 1.81: 48 Bond restraints: 6395 Sorted by residual: bond pdb=" O4 PX6 A1704 " pdb=" P1 PX6 A1704 " ideal model delta sigma weight residual 1.705 1.615 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" N VAL A 957 " pdb=" CA VAL A 957 " ideal model delta sigma weight residual 1.457 1.492 -0.035 9.00e-03 1.23e+04 1.49e+01 bond pdb=" C1 PX6 A1704 " pdb=" O4 PX6 A1704 " ideal model delta sigma weight residual 1.387 1.454 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C ARG A 894 " pdb=" N VAL A 895 " ideal model delta sigma weight residual 1.329 1.299 0.030 1.00e-02 1.00e+04 8.90e+00 bond pdb=" N VAL A 955 " pdb=" CA VAL A 955 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.37e+00 ... (remaining 6390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 8512 1.60 - 3.20: 145 3.20 - 4.81: 33 4.81 - 6.41: 10 6.41 - 8.01: 2 Bond angle restraints: 8702 Sorted by residual: angle pdb=" C TYR A 956 " pdb=" N VAL A 957 " pdb=" CA VAL A 957 " ideal model delta sigma weight residual 123.33 120.23 3.10 8.70e-01 1.32e+00 1.27e+01 angle pdb=" CA ARG A 894 " pdb=" C ARG A 894 " pdb=" O ARG A 894 " ideal model delta sigma weight residual 120.38 116.99 3.39 1.09e+00 8.42e-01 9.65e+00 angle pdb=" CA PRO A 958 " pdb=" C PRO A 958 " pdb=" N PRO A 959 " ideal model delta sigma weight residual 117.93 121.58 -3.65 1.20e+00 6.94e-01 9.26e+00 angle pdb=" C ARG A 894 " pdb=" N VAL A 895 " pdb=" CA VAL A 895 " ideal model delta sigma weight residual 121.88 126.27 -4.39 1.63e+00 3.76e-01 7.26e+00 angle pdb=" CA ARG A 894 " pdb=" C ARG A 894 " pdb=" N VAL A 895 " ideal model delta sigma weight residual 116.28 119.57 -3.29 1.26e+00 6.30e-01 6.83e+00 ... (remaining 8697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3342 17.86 - 35.72: 301 35.72 - 53.58: 79 53.58 - 71.44: 30 71.44 - 89.30: 4 Dihedral angle restraints: 3756 sinusoidal: 1178 harmonic: 2578 Sorted by residual: dihedral pdb=" CA TYR A 965 " pdb=" C TYR A 965 " pdb=" N MET A 966 " pdb=" CA MET A 966 " ideal model delta harmonic sigma weight residual 180.00 163.24 16.76 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" N ASN A 150 " pdb=" CA ASN A 150 " pdb=" CB ASN A 150 " pdb=" CG ASN A 150 " ideal model delta sinusoidal sigma weight residual -180.00 -120.21 -59.79 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 225 " pdb=" CB ARG A 225 " pdb=" CG ARG A 225 " pdb=" CD ARG A 225 " ideal model delta sinusoidal sigma weight residual 180.00 120.44 59.56 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 834 0.049 - 0.097: 184 0.097 - 0.146: 25 0.146 - 0.194: 2 0.194 - 0.243: 1 Chirality restraints: 1046 Sorted by residual: chirality pdb=" CA ARG A 894 " pdb=" N ARG A 894 " pdb=" C ARG A 894 " pdb=" CB ARG A 894 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL A 955 " pdb=" CA VAL A 955 " pdb=" CG1 VAL A 955 " pdb=" CG2 VAL A 955 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" C2 PX6 A1704 " pdb=" C1 PX6 A1704 " pdb=" C3 PX6 A1704 " pdb=" O7 PX6 A1704 " both_signs ideal model delta sigma weight residual False -2.32 -2.46 0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 1043 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 PCW A1703 " -0.072 2.00e-02 2.50e+03 7.11e-02 5.06e+01 pdb=" C19 PCW A1703 " 0.076 2.00e-02 2.50e+03 pdb=" C20 PCW A1703 " 0.066 2.00e-02 2.50e+03 pdb=" C21 PCW A1703 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 PCW A1703 " 0.058 2.00e-02 2.50e+03 5.85e-02 3.42e+01 pdb=" C39 PCW A1703 " -0.055 2.00e-02 2.50e+03 pdb=" C40 PCW A1703 " -0.062 2.00e-02 2.50e+03 pdb=" C41 PCW A1703 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW A1702 " 0.048 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C19 PCW A1702 " -0.050 2.00e-02 2.50e+03 pdb=" C20 PCW A1702 " -0.044 2.00e-02 2.50e+03 pdb=" C21 PCW A1702 " 0.046 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2122 2.84 - 3.35: 5987 3.35 - 3.87: 9636 3.87 - 4.38: 9268 4.38 - 4.90: 17838 Nonbonded interactions: 44851 Sorted by model distance: nonbonded pdb=" NZ LYS A 154 " pdb=" O2P PCW A1702 " model vdw 2.325 3.120 nonbonded pdb=" O LYS A 567 " pdb=" ND1 HIS A 568 " model vdw 2.340 3.120 nonbonded pdb=" OG SER A1024 " pdb=" OD1 ASN A1029 " model vdw 2.390 3.040 nonbonded pdb=" N ASP A 169 " pdb=" OD1 ASP A 169 " model vdw 2.419 3.120 nonbonded pdb=" O TRP A 781 " pdb=" OG1 THR A 785 " model vdw 2.441 3.040 ... (remaining 44846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.480 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.004 0.090 6395 Z= 0.224 Angle : 0.548 8.011 8702 Z= 0.281 Chirality : 0.039 0.243 1046 Planarity : 0.005 0.071 1080 Dihedral : 16.235 89.305 2082 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.40 % Allowed : 28.63 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.27 (0.30), residues: 856 helix: 2.85 (0.21), residues: 616 sheet: -1.30 (1.31), residues: 16 loop : -2.43 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 702 TYR 0.013 0.001 TYR A 965 PHE 0.010 0.001 PHE A 496 TRP 0.008 0.001 TRP A 149 HIS 0.004 0.001 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.22 ( 6395) covalent geometry : angle 0.54816 / 0.28 ( 8702) hydrogen bonds : bond 0.12320 / 8.38 ( 492) hydrogen bonds : angle 4.36927 / 3.30 ( 1458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.229 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 0.0458 time to fit residues: 4.6389 Evaluate side-chains 64 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 50.0000 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 50.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.194787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.167094 restraints weight = 9292.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.164318 restraints weight = 13039.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.158694 restraints weight = 13007.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.152749 restraints weight = 11979.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.153036 restraints weight = 11874.399| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6395 Z= 0.114 Angle : 0.454 6.104 8702 Z= 0.240 Chirality : 0.037 0.131 1046 Planarity : 0.004 0.039 1080 Dihedral : 8.352 85.536 1063 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.61 % Allowed : 27.22 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.51 (0.30), residues: 856 helix: 2.94 (0.21), residues: 631 sheet: -1.10 (1.34), residues: 16 loop : -2.47 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 601 TYR 0.013 0.001 TYR A 965 PHE 0.013 0.001 PHE A 993 TRP 0.008 0.001 TRP A 149 HIS 0.005 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 6395) covalent geometry : angle 0.45417 / 0.24 ( 8702) hydrogen bonds : bond 0.04512 / 3.09 ( 492) hydrogen bonds : angle 3.85029 / 2.91 ( 1458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 644 MET cc_start: 0.8147 (mtm) cc_final: 0.7945 (mtp) REVERT: A 893 MET cc_start: 0.8040 (mtp) cc_final: 0.7668 (mtp) outliers start: 8 outliers final: 4 residues processed: 68 average time/residue: 0.0443 time to fit residues: 4.4893 Evaluate side-chains 65 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 696 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 52 optimal weight: 40.0000 chunk 79 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 82 optimal weight: 50.0000 chunk 3 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 40.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.194511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.166042 restraints weight = 9228.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.163470 restraints weight = 13518.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.163488 restraints weight = 12948.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.161639 restraints weight = 10688.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.161229 restraints weight = 10378.127| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6395 Z= 0.115 Angle : 0.451 5.702 8702 Z= 0.236 Chirality : 0.037 0.125 1046 Planarity : 0.004 0.040 1080 Dihedral : 7.910 88.735 1061 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.81 % Allowed : 27.02 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.69 (0.30), residues: 856 helix: 3.05 (0.21), residues: 630 sheet: -0.51 (1.43), residues: 16 loop : -2.35 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 601 TYR 0.014 0.001 TYR A 965 PHE 0.009 0.001 PHE A 614 TRP 0.008 0.001 TRP A 149 HIS 0.005 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 6395) covalent geometry : angle 0.45149 / 0.24 ( 8702) hydrogen bonds : bond 0.04358 / 3.02 ( 492) hydrogen bonds : angle 3.69691 / 2.79 ( 1458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 566 MET cc_start: 0.8315 (mmm) cc_final: 0.8043 (tpt) REVERT: A 686 MET cc_start: 0.9012 (mmt) cc_final: 0.8802 (mmt) outliers start: 9 outliers final: 6 residues processed: 70 average time/residue: 0.0410 time to fit residues: 4.2531 Evaluate side-chains 66 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 900 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 74 optimal weight: 50.0000 chunk 56 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.191509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.163747 restraints weight = 9258.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.159576 restraints weight = 16053.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.156973 restraints weight = 16188.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.156071 restraints weight = 13946.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.156386 restraints weight = 11184.114| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6395 Z= 0.152 Angle : 0.487 5.318 8702 Z= 0.257 Chirality : 0.039 0.129 1046 Planarity : 0.004 0.040 1080 Dihedral : 8.467 81.307 1061 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.43 % Allowed : 27.22 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.64 (0.30), residues: 856 helix: 3.04 (0.21), residues: 628 sheet: -0.55 (1.39), residues: 16 loop : -2.37 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 710 TYR 0.015 0.001 TYR A 965 PHE 0.011 0.001 PHE A 647 TRP 0.008 0.001 TRP A 149 HIS 0.005 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 6395) covalent geometry : angle 0.48726 / 0.26 ( 8702) hydrogen bonds : bond 0.04999 / 3.49 ( 492) hydrogen bonds : angle 3.76963 / 2.85 ( 1458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 686 MET cc_start: 0.8713 (mmt) cc_final: 0.8421 (mmt) outliers start: 17 outliers final: 7 residues processed: 74 average time/residue: 0.0410 time to fit residues: 4.5371 Evaluate side-chains 67 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 963 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 50.0000 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.194077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.166338 restraints weight = 9332.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.163880 restraints weight = 13581.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.163004 restraints weight = 13208.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.160178 restraints weight = 12256.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.160896 restraints weight = 11620.405| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6395 Z= 0.113 Angle : 0.448 6.418 8702 Z= 0.234 Chirality : 0.037 0.131 1046 Planarity : 0.003 0.039 1080 Dihedral : 8.331 85.877 1061 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.42 % Allowed : 29.44 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.78 (0.30), residues: 856 helix: 3.12 (0.21), residues: 629 sheet: -0.49 (1.37), residues: 16 loop : -2.28 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 610 TYR 0.015 0.001 TYR A 965 PHE 0.009 0.001 PHE A 614 TRP 0.007 0.001 TRP A 149 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 6395) covalent geometry : angle 0.44767 / 0.23 ( 8702) hydrogen bonds : bond 0.04257 / 2.97 ( 492) hydrogen bonds : angle 3.63597 / 2.74 ( 1458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 686 MET cc_start: 0.8902 (mmt) cc_final: 0.8565 (mmt) outliers start: 12 outliers final: 6 residues processed: 70 average time/residue: 0.0428 time to fit residues: 4.4942 Evaluate side-chains 67 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 900 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 86 optimal weight: 40.0000 chunk 25 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.189736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.160669 restraints weight = 9415.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.158758 restraints weight = 17006.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.159431 restraints weight = 14648.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.157791 restraints weight = 9999.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.158600 restraints weight = 9577.975| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6395 Z= 0.182 Angle : 0.525 5.458 8702 Z= 0.275 Chirality : 0.040 0.135 1046 Planarity : 0.004 0.041 1080 Dihedral : 8.980 88.648 1061 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.02 % Allowed : 28.83 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.64 (0.30), residues: 856 helix: 3.05 (0.21), residues: 625 sheet: -0.54 (1.36), residues: 16 loop : -2.32 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 702 TYR 0.015 0.001 TYR A 965 PHE 0.013 0.001 PHE A 647 TRP 0.009 0.001 TRP A 149 HIS 0.006 0.001 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 ( 6395) covalent geometry : angle 0.52473 / 0.27 ( 8702) hydrogen bonds : bond 0.05291 / 3.69 ( 492) hydrogen bonds : angle 3.79807 / 2.87 ( 1458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 686 MET cc_start: 0.8996 (mmt) cc_final: 0.8611 (mmt) outliers start: 15 outliers final: 9 residues processed: 75 average time/residue: 0.0584 time to fit residues: 6.4858 Evaluate side-chains 71 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 983 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.194075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.168390 restraints weight = 9233.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.162359 restraints weight = 13923.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.155863 restraints weight = 11897.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.154725 restraints weight = 14438.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154860 restraints weight = 11360.270| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6395 Z= 0.112 Angle : 0.465 7.824 8702 Z= 0.239 Chirality : 0.038 0.133 1046 Planarity : 0.004 0.040 1080 Dihedral : 8.756 86.322 1061 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.62 % Allowed : 29.44 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.82 (0.30), residues: 856 helix: 3.15 (0.21), residues: 628 sheet: -0.33 (1.40), residues: 16 loop : -2.27 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 702 TYR 0.014 0.001 TYR A 965 PHE 0.010 0.001 PHE A 614 TRP 0.007 0.001 TRP A 149 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 6395) covalent geometry : angle 0.46497 / 0.24 ( 8702) hydrogen bonds : bond 0.04243 / 2.97 ( 492) hydrogen bonds : angle 3.59630 / 2.71 ( 1458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 686 MET cc_start: 0.8933 (mmt) cc_final: 0.8526 (mmt) outliers start: 13 outliers final: 9 residues processed: 76 average time/residue: 0.0605 time to fit residues: 6.8307 Evaluate side-chains 74 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 963 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 80 optimal weight: 30.0000 chunk 12 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.195130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.170037 restraints weight = 9328.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.167209 restraints weight = 13949.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.162179 restraints weight = 14638.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.162060 restraints weight = 15244.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.161967 restraints weight = 11047.467| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6395 Z= 0.108 Angle : 0.479 10.722 8702 Z= 0.241 Chirality : 0.037 0.126 1046 Planarity : 0.004 0.040 1080 Dihedral : 8.651 88.189 1061 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.22 % Allowed : 29.44 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.86 (0.30), residues: 856 helix: 3.17 (0.21), residues: 630 sheet: -0.23 (1.43), residues: 16 loop : -2.28 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 702 TYR 0.013 0.001 TYR A 965 PHE 0.009 0.001 PHE A 614 TRP 0.007 0.001 TRP A 149 HIS 0.005 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 6395) covalent geometry : angle 0.47866 / 0.24 ( 8702) hydrogen bonds : bond 0.04075 / 2.85 ( 492) hydrogen bonds : angle 3.54718 / 2.67 ( 1458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 686 MET cc_start: 0.8943 (mmt) cc_final: 0.8586 (mmt) outliers start: 11 outliers final: 10 residues processed: 74 average time/residue: 0.0579 time to fit residues: 6.4159 Evaluate side-chains 75 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1040 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 26 optimal weight: 0.0270 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.0270 chunk 63 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.197136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.169449 restraints weight = 9380.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.166371 restraints weight = 14029.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.165108 restraints weight = 14042.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.163105 restraints weight = 14525.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.164001 restraints weight = 12036.814| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6395 Z= 0.096 Angle : 0.452 9.389 8702 Z= 0.228 Chirality : 0.037 0.129 1046 Planarity : 0.003 0.039 1080 Dihedral : 8.430 89.464 1061 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.22 % Allowed : 29.64 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.97 (0.30), residues: 856 helix: 3.26 (0.20), residues: 630 sheet: -0.10 (1.46), residues: 16 loop : -2.27 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 702 TYR 0.012 0.001 TYR A 965 PHE 0.008 0.001 PHE A 614 TRP 0.007 0.001 TRP A 149 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 ( 6395) covalent geometry : angle 0.45204 / 0.23 ( 8702) hydrogen bonds : bond 0.03639 / 2.54 ( 492) hydrogen bonds : angle 3.43884 / 2.58 ( 1458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 686 MET cc_start: 0.8952 (mmt) cc_final: 0.8602 (mmt) outliers start: 11 outliers final: 10 residues processed: 75 average time/residue: 0.0603 time to fit residues: 7.0758 Evaluate side-chains 74 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1040 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 66 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 53 optimal weight: 50.0000 chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 87 optimal weight: 50.0000 chunk 28 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.196061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.168730 restraints weight = 9266.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.165657 restraints weight = 15355.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.163751 restraints weight = 14188.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.162685 restraints weight = 13458.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.163337 restraints weight = 11060.757| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6395 Z= 0.110 Angle : 0.470 9.211 8702 Z= 0.237 Chirality : 0.037 0.125 1046 Planarity : 0.004 0.039 1080 Dihedral : 8.439 86.962 1061 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.02 % Allowed : 30.44 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.95 (0.30), residues: 856 helix: 3.25 (0.20), residues: 630 sheet: -0.09 (1.47), residues: 16 loop : -2.28 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 702 TYR 0.012 0.001 TYR A 965 PHE 0.009 0.001 PHE A 647 TRP 0.008 0.001 TRP A 149 HIS 0.005 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 6395) covalent geometry : angle 0.46982 / 0.24 ( 8702) hydrogen bonds : bond 0.03936 / 2.75 ( 492) hydrogen bonds : angle 3.47228 / 2.61 ( 1458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 686 MET cc_start: 0.8937 (mmt) cc_final: 0.8580 (mmt) outliers start: 10 outliers final: 10 residues processed: 72 average time/residue: 0.0463 time to fit residues: 4.9544 Evaluate side-chains 74 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1040 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 19 optimal weight: 0.0370 chunk 18 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.194650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.166510 restraints weight = 9405.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.164182 restraints weight = 14953.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.163602 restraints weight = 13869.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.162014 restraints weight = 13115.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.162213 restraints weight = 11644.126| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6395 Z= 0.122 Angle : 0.489 9.330 8702 Z= 0.247 Chirality : 0.038 0.126 1046 Planarity : 0.004 0.040 1080 Dihedral : 8.484 84.702 1061 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.22 % Allowed : 30.04 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.91 (0.30), residues: 856 helix: 3.21 (0.20), residues: 630 sheet: -0.08 (1.48), residues: 16 loop : -2.28 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 702 TYR 0.013 0.001 TYR A 965 PHE 0.009 0.001 PHE A 647 TRP 0.008 0.001 TRP A 149 HIS 0.005 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 6395) covalent geometry : angle 0.48893 / 0.25 ( 8702) hydrogen bonds : bond 0.04257 / 2.97 ( 492) hydrogen bonds : angle 3.51284 / 2.64 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1026.79 seconds wall clock time: 18 minutes 20.48 seconds (1100.48 seconds total)