Starting phenix.real_space_refine on Tue Aug 4 21:52:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pda_17608/08_2026/8pda_17608.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pda_17608/08_2026/8pda_17608.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/8pda_17608/08_2026/8pda_17608.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pda_17608/08_2026/8pda_17608.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pda_17608/08_2026/8pda_17608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pda_17608/08_2026/8pda_17608.map" model { file = "/net/cci-nas-00/data/ceres_data/8pda_17608/08_2026/8pda_17608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pda_17608/08_2026/8pda_17608.cif" } 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 4413 2.51 5 N 1110 2.21 5 O 1180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6736 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 6563 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 378} Link IDs: {'PTRANS': 38, 'TRANS': 934} Chain breaks: 11 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1456 Unresolved non-hydrogen angles: 1867 Unresolved non-hydrogen dihedrals: 1257 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'PHE:plan': 30, 'ASN:plan1': 18, 'ASP:plan': 20, 'ARG:plan': 18, 'GLU:plan': 28, 'HIS:plan': 10, 'TYR:plan': 20, 'TRP:plan': 9, 'GLN:plan1': 9} Unresolved non-hydrogen planarities: 803 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: 1.25, per 1000 atoms: 0.19 Number of scatterers: 6736 At special positions: 0 Unit cell: (111.507, 97.888, 137.894, 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 1180 8.00 N 1110 7.00 C 4413 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 339.0 milliseconds 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1850 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 2 sheets defined 74.5% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 67 through 77 Processing helix chain 'A' and resid 113 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) 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 1309 removed outlier: 3.708A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A1305 " --> pdb=" O VAL A1301 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A1309 " --> pdb=" O VAL A1305 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, 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) 505 hydrogen bonds defined for protein. 1488 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: 0.72 Time building geometry restraints manager: 0.57 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: 1097 1.32 - 1.44: 1760 1.44 - 1.57: 3946 1.57 - 1.69: 7 1.69 - 1.81: 48 Bond restraints: 6858 Sorted by residual: bond pdb=" C GLU A1304 " pdb=" O GLU A1304 " ideal model delta sigma weight residual 1.237 1.316 -0.079 1.17e-02 7.31e+03 4.57e+01 bond pdb=" CA SER A 799 " pdb=" CB SER A 799 " ideal model delta sigma weight residual 1.526 1.456 0.070 1.51e-02 4.39e+03 2.13e+01 bond pdb=" CA SER A 800 " pdb=" CB SER A 800 " ideal model delta sigma weight residual 1.537 1.457 0.081 1.76e-02 3.23e+03 2.09e+01 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 ILE A 111 " pdb=" CA ILE A 111 " ideal model delta sigma weight residual 1.461 1.510 -0.049 1.23e-02 6.61e+03 1.57e+01 ... (remaining 6853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 8797 1.60 - 3.20: 453 3.20 - 4.81: 78 4.81 - 6.41: 17 6.41 - 8.01: 3 Bond angle restraints: 9348 Sorted by residual: angle pdb=" CA GLU A 798 " pdb=" C GLU A 798 " pdb=" N SER A 799 " ideal model delta sigma weight residual 117.30 123.36 -6.06 1.16e+00 7.43e-01 2.73e+01 angle pdb=" N VAL A 803 " pdb=" CA VAL A 803 " pdb=" C VAL A 803 " ideal model delta sigma weight residual 112.12 108.35 3.77 8.40e-01 1.42e+00 2.02e+01 angle pdb=" O GLU A 798 " pdb=" C GLU A 798 " pdb=" N SER A 799 " ideal model delta sigma weight residual 122.12 117.52 4.60 1.06e+00 8.90e-01 1.88e+01 angle pdb=" N TYR A 802 " pdb=" CA TYR A 802 " pdb=" C TYR A 802 " ideal model delta sigma weight residual 111.56 105.70 5.86 1.38e+00 5.25e-01 1.80e+01 angle pdb=" C GLU A 798 " pdb=" N SER A 799 " pdb=" CA SER A 799 " ideal model delta sigma weight residual 122.06 116.43 5.63 1.39e+00 5.18e-01 1.64e+01 ... (remaining 9343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3615 17.86 - 35.72: 300 35.72 - 53.58: 79 53.58 - 71.44: 30 71.44 - 89.30: 4 Dihedral angle restraints: 4028 sinusoidal: 1181 harmonic: 2847 Sorted by residual: dihedral pdb=" C HIS A 94 " pdb=" N HIS A 94 " pdb=" CA HIS A 94 " pdb=" CB HIS A 94 " ideal model delta harmonic sigma weight residual -122.60 -133.00 10.40 0 2.50e+00 1.60e-01 1.73e+01 dihedral pdb=" CA MET A 65 " pdb=" C MET A 65 " pdb=" N HIS A 66 " pdb=" CA HIS A 66 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 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 ... (remaining 4025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 996 0.072 - 0.143: 108 0.143 - 0.215: 25 0.215 - 0.287: 3 0.287 - 0.358: 2 Chirality restraints: 1134 Sorted by residual: chirality pdb=" CA HIS A 94 " pdb=" N HIS A 94 " pdb=" C HIS A 94 " pdb=" CB HIS A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ARG A 43 " pdb=" N ARG A 43 " pdb=" C ARG A 43 " pdb=" CB ARG A 43 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 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 ... (remaining 1131 not shown) Planarity restraints: 1174 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=" CA ILE A 111 " 0.025 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C ILE A 111 " -0.082 2.00e-02 2.50e+03 pdb=" O ILE A 111 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO A 112 " 0.029 2.00e-02 2.50e+03 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 843 2.75 - 3.29: 6419 3.29 - 3.83: 10670 3.83 - 4.36: 10161 4.36 - 4.90: 19512 Nonbonded interactions: 47605 Sorted by model distance: nonbonded pdb=" O GLN A 98 " pdb=" CB GLU A1313 " model vdw 2.217 3.440 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 ... (remaining 47600 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: 2.260 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.100 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 0.090 6858 Z= 0.422 Angle : 0.769 8.011 9348 Z= 0.514 Chirality : 0.053 0.358 1134 Planarity : 0.006 0.071 1174 Dihedral : 15.905 89.305 2178 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.40 % Allowed : 28.77 % Favored : 70.82 % 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: 1.89 (0.28), residues: 949 helix: 2.79 (0.21), residues: 635 sheet: -1.30 (1.31), residues: 16 loop : -2.25 (0.32), residues: 298 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 0.00610 / 0.42 ( 6858) covalent geometry : angle 0.76903 / 0.51 ( 9348) hydrogen bonds : bond 0.11924 / 8.88 ( 505) hydrogen bonds : angle 4.51060 / 3.40 ( 1488) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.167 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 75 average time/residue: 0.0470 time to fit residues: 5.1968 Evaluate side-chains 69 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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: 97 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.0370 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 50.0000 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 = 0.4385 r_free = 0.4385 target = 0.199315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.166640 restraints weight = 10110.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.164041 restraints weight = 17687.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.162918 restraints weight = 14575.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.160732 restraints weight = 10974.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.161596 restraints weight = 8628.620| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6858 Z= 0.110 Angle : 0.451 6.053 9348 Z= 0.240 Chirality : 0.037 0.130 1134 Planarity : 0.004 0.038 1174 Dihedral : 8.001 85.858 1156 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.81 % Allowed : 27.36 % Favored : 70.82 % 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: 2.22 (0.28), residues: 949 helix: 2.85 (0.20), residues: 652 sheet: -1.05 (1.36), residues: 16 loop : -1.94 (0.35), residues: 281 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 0.012 0.001 PHE A 993 TRP 0.008 0.001 TRP A 149 HIS 0.005 0.001 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 6858) covalent geometry : angle 0.45087 / 0.24 ( 9348) hydrogen bonds : bond 0.04333 / 3.25 ( 505) hydrogen bonds : angle 3.83405 / 2.89 ( 1488) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 893 MET cc_start: 0.8117 (mtp) cc_final: 0.7779 (mtp) outliers start: 9 outliers final: 4 residues processed: 73 average time/residue: 0.0528 time to fit residues: 5.7677 Evaluate side-chains 69 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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: 97 random chunks: chunk 85 optimal weight: 50.0000 chunk 58 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 chunk 59 optimal weight: 9.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.188479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.153924 restraints weight = 10153.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.147773 restraints weight = 20701.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.142463 restraints weight = 15502.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141064 restraints weight = 14278.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141054 restraints weight = 13557.701| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 6858 Z= 0.328 Angle : 0.684 6.389 9348 Z= 0.360 Chirality : 0.045 0.166 1134 Planarity : 0.005 0.050 1174 Dihedral : 9.657 88.948 1154 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 6.24 % Allowed : 25.35 % Favored : 68.41 % 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: 1.83 (0.28), residues: 949 helix: 2.58 (0.20), residues: 640 sheet: -1.43 (1.32), residues: 16 loop : -1.93 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 702 TYR 0.019 0.002 TYR A1027 PHE 0.020 0.002 PHE A 647 TRP 0.014 0.002 TRP A 662 HIS 0.007 0.002 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00805 / 0.33 ( 6858) covalent geometry : angle 0.68382 / 0.36 ( 9348) hydrogen bonds : bond 0.07041 / 5.25 ( 505) hydrogen bonds : angle 4.30067 / 3.23 ( 1488) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.212 Fit side-chains REVERT: A 807 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7453 (mp) outliers start: 31 outliers final: 18 residues processed: 86 average time/residue: 0.0400 time to fit residues: 5.2963 Evaluate side-chains 78 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 504 ILE 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 754 THR Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 802 TYR Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 983 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 41 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 chunk 85 optimal weight: 50.0000 chunk 1 optimal weight: 30.0000 chunk 74 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.194839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.155593 restraints weight = 10098.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.150578 restraints weight = 17978.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.152630 restraints weight = 13238.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.152689 restraints weight = 7621.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.153227 restraints weight = 6787.261| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6858 Z= 0.125 Angle : 0.472 5.391 9348 Z= 0.251 Chirality : 0.038 0.141 1134 Planarity : 0.004 0.046 1174 Dihedral : 8.937 85.978 1154 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.22 % Allowed : 28.77 % Favored : 68.01 % 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: 2.20 (0.28), residues: 949 helix: 2.80 (0.20), residues: 644 sheet: -1.33 (1.30), residues: 16 loop : -1.69 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 610 TYR 0.016 0.001 TYR A 965 PHE 0.012 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 0.00271 / 0.13 ( 6858) covalent geometry : angle 0.47222 / 0.25 ( 9348) hydrogen bonds : bond 0.04931 / 3.70 ( 505) hydrogen bonds : angle 3.84452 / 2.90 ( 1488) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.235 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 73 average time/residue: 0.0512 time to fit residues: 5.7931 Evaluate side-chains 69 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 TYR Chi-restraints excluded: chain A residue 900 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 31 optimal weight: 0.0870 chunk 57 optimal weight: 0.1980 chunk 94 optimal weight: 50.0000 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1029 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.206578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.173779 restraints weight = 10088.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.173648 restraints weight = 17719.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.174143 restraints weight = 14994.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.173551 restraints weight = 9031.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.174069 restraints weight = 8198.646| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6858 Z= 0.095 Angle : 0.433 7.062 9348 Z= 0.226 Chirality : 0.037 0.134 1134 Planarity : 0.004 0.039 1174 Dihedral : 8.483 88.215 1154 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.62 % Allowed : 30.18 % Favored : 67.20 % 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: 2.50 (0.28), residues: 949 helix: 3.07 (0.20), residues: 642 sheet: -0.57 (1.43), residues: 16 loop : -1.69 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 601 TYR 0.013 0.001 TYR A 965 PHE 0.012 0.001 PHE A 993 TRP 0.006 0.001 TRP A 149 HIS 0.005 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.10 ( 6858) covalent geometry : angle 0.43273 / 0.23 ( 9348) hydrogen bonds : bond 0.03723 / 2.80 ( 505) hydrogen bonds : angle 3.58054 / 2.72 ( 1488) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.154 Fit side-chains REVERT: A 966 MET cc_start: 0.7635 (mmm) cc_final: 0.7347 (mtp) outliers start: 13 outliers final: 9 residues processed: 75 average time/residue: 0.0390 time to fit residues: 4.5120 Evaluate side-chains 72 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 674 SER Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 802 TYR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1040 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 37 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 1 optimal weight: 50.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.204108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.170603 restraints weight = 10067.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.168640 restraints weight = 17201.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.169690 restraints weight = 15253.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.168808 restraints weight = 9389.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.169383 restraints weight = 8440.795| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6858 Z= 0.111 Angle : 0.447 5.566 9348 Z= 0.233 Chirality : 0.038 0.126 1134 Planarity : 0.003 0.040 1174 Dihedral : 8.401 89.345 1154 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.41 % Allowed : 30.58 % Favored : 67.00 % 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: 2.59 (0.29), residues: 949 helix: 3.10 (0.20), residues: 645 sheet: -0.39 (1.45), residues: 16 loop : -1.61 (0.35), residues: 288 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 0.007 0.001 TRP A 149 HIS 0.005 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 6858) covalent geometry : angle 0.44687 / 0.23 ( 9348) hydrogen bonds : bond 0.04136 / 3.11 ( 505) hydrogen bonds : angle 3.58918 / 2.72 ( 1488) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.178 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 77 average time/residue: 0.0483 time to fit residues: 5.6856 Evaluate side-chains 77 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 665 SER 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 802 TYR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1040 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 30.0000 chunk 90 optimal weight: 7.9990 chunk 2 optimal weight: 50.0000 chunk 54 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 50.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.4378 r_free = 0.4378 target = 0.199211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.164260 restraints weight = 10061.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.162105 restraints weight = 19082.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.161991 restraints weight = 15466.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.160513 restraints weight = 10134.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.161237 restraints weight = 8615.653| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6858 Z= 0.176 Angle : 0.520 5.422 9348 Z= 0.272 Chirality : 0.040 0.134 1134 Planarity : 0.004 0.042 1174 Dihedral : 8.600 78.249 1154 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.82 % Allowed : 29.98 % Favored : 66.20 % 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: 2.45 (0.29), residues: 949 helix: 2.97 (0.20), residues: 643 sheet: -0.50 (1.42), residues: 16 loop : -1.57 (0.35), residues: 290 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 0.00427 / 0.18 ( 6858) covalent geometry : angle 0.52008 / 0.27 ( 9348) hydrogen bonds : bond 0.05298 / 3.97 ( 505) hydrogen bonds : angle 3.78236 / 2.86 ( 1488) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.223 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 79 average time/residue: 0.0404 time to fit residues: 5.0388 Evaluate side-chains 75 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 492 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 665 SER Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 TYR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1040 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 64 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 61 optimal weight: 40.0000 chunk 87 optimal weight: 50.0000 chunk 8 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.200258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.168620 restraints weight = 10162.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157827 restraints weight = 17739.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.153469 restraints weight = 11967.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.148582 restraints weight = 14387.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149538 restraints weight = 14031.560| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6858 Z= 0.160 Angle : 0.501 5.604 9348 Z= 0.262 Chirality : 0.039 0.128 1134 Planarity : 0.004 0.043 1174 Dihedral : 8.540 80.819 1154 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.02 % Allowed : 30.58 % Favored : 66.40 % 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: 2.52 (0.28), residues: 949 helix: 3.03 (0.20), residues: 638 sheet: -0.42 (1.45), residues: 16 loop : -1.46 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 702 TYR 0.015 0.001 TYR A 965 PHE 0.012 0.001 PHE A 614 TRP 0.008 0.001 TRP A 149 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 6858) covalent geometry : angle 0.50114 / 0.26 ( 9348) hydrogen bonds : bond 0.04996 / 3.74 ( 505) hydrogen bonds : angle 3.73867 / 2.83 ( 1488) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.257 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 79 average time/residue: 0.0522 time to fit residues: 6.4295 Evaluate side-chains 79 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 228 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 TYR 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: 97 random chunks: chunk 94 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 0.0040 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 50.0000 chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.199440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.164903 restraints weight = 10132.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.163846 restraints weight = 17927.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.163663 restraints weight = 15281.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.162045 restraints weight = 10222.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.162710 restraints weight = 8829.407| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6858 Z= 0.166 Angle : 0.516 6.113 9348 Z= 0.270 Chirality : 0.040 0.127 1134 Planarity : 0.004 0.043 1174 Dihedral : 8.535 78.747 1154 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.62 % Allowed : 30.18 % Favored : 66.20 % 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: 2.50 (0.28), residues: 949 helix: 2.99 (0.20), residues: 639 sheet: -0.42 (1.44), residues: 16 loop : -1.44 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 702 TYR 0.015 0.001 TYR A 965 PHE 0.012 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 0.00398 / 0.17 ( 6858) covalent geometry : angle 0.51562 / 0.27 ( 9348) hydrogen bonds : bond 0.05167 / 3.87 ( 505) hydrogen bonds : angle 3.77240 / 2.85 ( 1488) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.189 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 78 average time/residue: 0.0457 time to fit residues: 5.5781 Evaluate side-chains 77 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 228 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 TYR 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: 97 random chunks: chunk 3 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 40.0000 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 18 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4424 r_free = 0.4424 target = 0.203224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.172180 restraints weight = 10039.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.168127 restraints weight = 17289.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.168489 restraints weight = 16591.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.167190 restraints weight = 9858.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.168016 restraints weight = 8114.654| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6858 Z= 0.111 Angle : 0.467 7.487 9348 Z= 0.241 Chirality : 0.038 0.134 1134 Planarity : 0.004 0.043 1174 Dihedral : 8.221 85.771 1154 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.41 % Allowed : 31.59 % Favored : 66.00 % 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: 2.72 (0.29), residues: 949 helix: 3.14 (0.20), residues: 643 sheet: -0.27 (1.45), residues: 16 loop : -1.38 (0.36), residues: 290 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 0.020 0.001 PHE A 993 TRP 0.006 0.001 TRP A 149 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 6858) covalent geometry : angle 0.46710 / 0.24 ( 9348) hydrogen bonds : bond 0.04218 / 3.17 ( 505) hydrogen bonds : angle 3.59062 / 2.73 ( 1488) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.259 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 76 average time/residue: 0.0542 time to fit residues: 6.4274 Evaluate side-chains 78 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 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 665 SER Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 TYR 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: 97 random chunks: chunk 81 optimal weight: 8.9990 chunk 1 optimal weight: 50.0000 chunk 62 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 95 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.196210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.167995 restraints weight = 10093.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.166978 restraints weight = 19589.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.165717 restraints weight = 17197.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.164687 restraints weight = 11732.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.165114 restraints weight = 9859.588| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 6858 Z= 0.251 Angle : 0.601 6.666 9348 Z= 0.314 Chirality : 0.043 0.146 1134 Planarity : 0.004 0.043 1174 Dihedral : 8.828 74.106 1154 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.82 % Allowed : 31.39 % Favored : 65.79 % 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: 2.39 (0.28), residues: 949 helix: 2.88 (0.20), residues: 641 sheet: -0.54 (1.46), residues: 16 loop : -1.42 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 702 TYR 0.017 0.002 TYR A1027 PHE 0.016 0.002 PHE A 993 TRP 0.011 0.002 TRP A 149 HIS 0.007 0.002 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.25 ( 6858) covalent geometry : angle 0.60082 / 0.31 ( 9348) hydrogen bonds : bond 0.06018 / 4.51 ( 505) hydrogen bonds : angle 3.93732 / 2.97 ( 1488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1016.68 seconds wall clock time: 18 minutes 5.31 seconds (1085.31 seconds total)