Starting phenix.real_space_refine on Wed Jun 11 05:07:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7trd_26086/06_2025/7trd_26086.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trd_26086/06_2025/7trd_26086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7trd_26086/06_2025/7trd_26086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trd_26086/06_2025/7trd_26086.map" model { file = "/net/cci-nas-00/data/ceres_data/7trd_26086/06_2025/7trd_26086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trd_26086/06_2025/7trd_26086.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 224 5.49 5 S 36 5.16 5 C 6931 2.51 5 N 2219 2.21 5 O 2830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12240 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 4605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 4605 Classifications: {'RNA': 217} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 21, 'rna3p_pur': 86, 'rna3p_pyr': 96} Link IDs: {'rna2p': 35, 'rna3p': 181} Chain breaks: 2 Chain: "A" Number of atoms: 7488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 934, 7488 Classifications: {'peptide': 934} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 877} Chain breaks: 4 Chain: "N" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 8.78, per 1000 atoms: 0.72 Number of scatterers: 12240 At special positions: 0 Unit cell: (108.9, 122.1, 108.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 224 15.00 O 2830 8.00 N 2219 7.00 C 6931 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: 3.31 Conformation dependent library (CDL) restraints added in 1.2 seconds 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 8 sheets defined 55.4% alpha, 15.2% beta 64 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 removed outlier: 3.604A pdb=" N ARG A 11 " --> pdb=" O CYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 76 through 92 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 146 through 156 Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.839A pdb=" N LEU A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 removed outlier: 3.999A pdb=" N LEU A 332 " --> pdb=" O LYS A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 353 through 366 removed outlier: 3.574A pdb=" N ALA A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 389 through 401 removed outlier: 4.037A pdb=" N PHE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.782A pdb=" N LEU A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 454 removed outlier: 3.781A pdb=" N GLN A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.716A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.506A pdb=" N GLU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.655A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 560 removed outlier: 3.764A pdb=" N HIS A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 4.387A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.515A pdb=" N GLU A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 672 removed outlier: 3.531A pdb=" N SER A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.651A pdb=" N LEU A 676 " --> pdb=" O PRO A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 698 removed outlier: 3.762A pdb=" N ILE A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 Processing helix chain 'A' and resid 765 through 769 removed outlier: 4.006A pdb=" N LEU A 769 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 removed outlier: 3.582A pdb=" N PHE A 776 " --> pdb=" O TYR A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 815 Processing helix chain 'A' and resid 837 through 854 Processing helix chain 'A' and resid 876 through 890 Processing helix chain 'A' and resid 946 through 950 removed outlier: 3.789A pdb=" N ALA A 950 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 958 removed outlier: 4.052A pdb=" N LEU A 958 " --> pdb=" O ARG A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 982 Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 993 through 1017 Processing helix chain 'A' and resid 1024 through 1027 Processing helix chain 'A' and resid 1028 through 1051 removed outlier: 4.120A pdb=" N PHE A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A1051 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1082 removed outlier: 4.323A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TRP A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.651A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Proline residue: A1091 - end of helix removed outlier: 4.508A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A1106 " --> pdb=" O GLN A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1119 removed outlier: 3.712A pdb=" N ALA A1119 " --> pdb=" O LEU A1115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 removed outlier: 6.418A pdb=" N LEU A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 160 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 168 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 14.579A pdb=" N CYS A 171 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 744 " --> pdb=" O LYS A 760 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 removed outlier: 6.418A pdb=" N LEU A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 160 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 168 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 14.579A pdb=" N CYS A 171 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA6, first strand: chain 'A' and resid 598 through 600 removed outlier: 6.601A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 862 through 865 removed outlier: 3.640A pdb=" N VAL A 904 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP A 712 " --> pdb=" O LYS A 902 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS A 902 " --> pdb=" O ASP A 712 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 927 through 930 396 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 174 hydrogen bonds 332 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 7.49 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2612 1.33 - 1.45: 3958 1.45 - 1.57: 5907 1.57 - 1.69: 444 1.69 - 1.81: 47 Bond restraints: 12968 Sorted by residual: bond pdb=" C LYS A 973 " pdb=" N LEU A 974 " ideal model delta sigma weight residual 1.334 1.384 -0.049 1.27e-02 6.20e+03 1.50e+01 bond pdb=" N VAL A 697 " pdb=" CA VAL A 697 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.11e+00 bond pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.97e+00 bond pdb=" N ASN A 125 " pdb=" CA ASN A 125 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.22e-02 6.72e+03 6.26e+00 bond pdb=" N GLU A 705 " pdb=" CA GLU A 705 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.28e-02 6.10e+03 6.06e+00 ... (remaining 12963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 17958 1.52 - 3.05: 595 3.05 - 4.57: 76 4.57 - 6.09: 14 6.09 - 7.61: 1 Bond angle restraints: 18644 Sorted by residual: angle pdb=" O LYS A 973 " pdb=" C LYS A 973 " pdb=" N LEU A 974 " ideal model delta sigma weight residual 122.07 117.19 4.88 1.03e+00 9.43e-01 2.25e+01 angle pdb=" N VAL A 596 " pdb=" CA VAL A 596 " pdb=" C VAL A 596 " ideal model delta sigma weight residual 112.43 108.61 3.82 9.20e-01 1.18e+00 1.73e+01 angle pdb=" CA LYS A 973 " pdb=" C LYS A 973 " pdb=" N LEU A 974 " ideal model delta sigma weight residual 117.07 121.64 -4.57 1.14e+00 7.69e-01 1.61e+01 angle pdb=" C LYS A 973 " pdb=" N LEU A 974 " pdb=" CA LEU A 974 " ideal model delta sigma weight residual 120.44 125.62 -5.18 1.30e+00 5.92e-01 1.59e+01 angle pdb=" N ASP A1038 " pdb=" CA ASP A1038 " pdb=" C ASP A1038 " ideal model delta sigma weight residual 113.28 109.10 4.18 1.22e+00 6.72e-01 1.18e+01 ... (remaining 18639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 7444 35.85 - 71.70: 614 71.70 - 107.56: 96 107.56 - 143.41: 4 143.41 - 179.26: 3 Dihedral angle restraints: 8161 sinusoidal: 5438 harmonic: 2723 Sorted by residual: dihedral pdb=" O4' U B 43 " pdb=" C1' U B 43 " pdb=" N1 U B 43 " pdb=" C2 U B 43 " ideal model delta sinusoidal sigma weight residual 232.00 52.74 179.26 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 133 " pdb=" C1' U B 133 " pdb=" N1 U B 133 " pdb=" C2 U B 133 " ideal model delta sinusoidal sigma weight residual -128.00 48.74 -176.74 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 291 " pdb=" C1' U B 291 " pdb=" N1 U B 291 " pdb=" C2 U B 291 " ideal model delta sinusoidal sigma weight residual -128.00 40.41 -168.41 1 1.70e+01 3.46e-03 6.58e+01 ... (remaining 8158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1913 0.048 - 0.095: 287 0.095 - 0.143: 61 0.143 - 0.190: 22 0.190 - 0.238: 2 Chirality restraints: 2285 Sorted by residual: chirality pdb=" P G B 130 " pdb=" OP1 G B 130 " pdb=" OP2 G B 130 " pdb=" O5' G B 130 " both_signs ideal model delta sigma weight residual True 2.41 -2.65 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1' A B 174 " pdb=" O4' A B 174 " pdb=" C2' A B 174 " pdb=" N9 A B 174 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' G B 130 " pdb=" C4' G B 130 " pdb=" O3' G B 130 " pdb=" C2' G B 130 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 2282 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 130 " -0.001 2.00e-02 2.50e+03 4.15e-02 5.17e+01 pdb=" N9 G B 130 " 0.002 2.00e-02 2.50e+03 pdb=" C8 G B 130 " -0.010 2.00e-02 2.50e+03 pdb=" N7 G B 130 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 130 " 0.036 2.00e-02 2.50e+03 pdb=" C6 G B 130 " -0.105 2.00e-02 2.50e+03 pdb=" O6 G B 130 " 0.069 2.00e-02 2.50e+03 pdb=" N1 G B 130 " -0.039 2.00e-02 2.50e+03 pdb=" C2 G B 130 " 0.046 2.00e-02 2.50e+03 pdb=" N2 G B 130 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G B 130 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G B 130 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 129 " 0.003 2.00e-02 2.50e+03 3.20e-02 2.82e+01 pdb=" N9 A B 129 " -0.003 2.00e-02 2.50e+03 pdb=" C8 A B 129 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A B 129 " -0.015 2.00e-02 2.50e+03 pdb=" C5 A B 129 " 0.075 2.00e-02 2.50e+03 pdb=" C6 A B 129 " 0.020 2.00e-02 2.50e+03 pdb=" N6 A B 129 " -0.014 2.00e-02 2.50e+03 pdb=" N1 A B 129 " -0.045 2.00e-02 2.50e+03 pdb=" C2 A B 129 " 0.031 2.00e-02 2.50e+03 pdb=" N3 A B 129 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A B 129 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 131 " -0.015 2.00e-02 2.50e+03 3.41e-02 2.62e+01 pdb=" N1 C B 131 " -0.012 2.00e-02 2.50e+03 pdb=" C2 C B 131 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C B 131 " -0.000 2.00e-02 2.50e+03 pdb=" N3 C B 131 " 0.007 2.00e-02 2.50e+03 pdb=" C4 C B 131 " 0.077 2.00e-02 2.50e+03 pdb=" N4 C B 131 " -0.064 2.00e-02 2.50e+03 pdb=" C5 C B 131 " 0.005 2.00e-02 2.50e+03 pdb=" C6 C B 131 " 0.001 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1470 2.74 - 3.28: 11066 3.28 - 3.82: 21444 3.82 - 4.36: 24209 4.36 - 4.90: 37863 Nonbonded interactions: 96052 Sorted by model distance: nonbonded pdb=" O LEU A1079 " pdb=" OG1 THR A1083 " model vdw 2.206 3.040 nonbonded pdb=" O2' G B 71 " pdb=" OP1 C B 72 " model vdw 2.242 3.040 nonbonded pdb=" OG SER A 619 " pdb=" O ASN A 635 " model vdw 2.261 3.040 nonbonded pdb=" O2' A B 175 " pdb=" OP1 A B 176 " model vdw 2.279 3.040 nonbonded pdb=" O2' U B 314 " pdb=" OE2 GLU A 538 " model vdw 2.293 3.040 ... (remaining 96047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 72.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.300 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 0.049 12968 Z= 0.213 Angle : 0.636 7.614 18644 Z= 0.378 Chirality : 0.039 0.238 2285 Planarity : 0.005 0.042 1542 Dihedral : 21.934 179.261 6395 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.12 % Allowed : 0.86 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.28), residues: 924 helix: 1.00 (0.26), residues: 443 sheet: -0.29 (0.51), residues: 93 loop : -1.25 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 581 HIS 0.011 0.001 HIS A 779 PHE 0.026 0.002 PHE A1021 TYR 0.009 0.001 TYR A 168 ARG 0.006 0.001 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.13344 ( 556) hydrogen bonds : angle 5.61174 ( 1463) covalent geometry : bond 0.00377 (12968) covalent geometry : angle 0.63569 (18644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 1.022 Fit side-chains REVERT: A 372 MET cc_start: 0.4197 (mmp) cc_final: 0.3919 (mmm) REVERT: A 700 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7503 (mt0) REVERT: A 1059 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8219 (ttmm) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.4144 time to fit residues: 27.2435 Evaluate side-chains 33 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 700 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 0.2980 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 HIS ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.144054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.087339 restraints weight = 22764.460| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.24 r_work: 0.2992 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12968 Z= 0.140 Angle : 0.574 8.638 18644 Z= 0.289 Chirality : 0.034 0.174 2285 Planarity : 0.005 0.037 1542 Dihedral : 23.394 179.923 4579 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.49 % Allowed : 5.67 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.29), residues: 924 helix: 1.34 (0.25), residues: 452 sheet: -0.18 (0.48), residues: 103 loop : -1.06 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 581 HIS 0.008 0.001 HIS A 779 PHE 0.016 0.001 PHE A1021 TYR 0.009 0.001 TYR A1044 ARG 0.007 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04860 ( 556) hydrogen bonds : angle 4.20341 ( 1463) covalent geometry : bond 0.00301 (12968) covalent geometry : angle 0.57443 (18644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 1.030 Fit side-chains REVERT: A 372 MET cc_start: 0.4935 (mmp) cc_final: 0.4665 (mmm) REVERT: A 712 ASP cc_start: 0.8332 (t0) cc_final: 0.8122 (t0) REVERT: A 1059 LYS cc_start: 0.8695 (ttmt) cc_final: 0.8338 (ttmm) outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.2267 time to fit residues: 15.3485 Evaluate side-chains 36 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 1016 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 46 optimal weight: 0.0000 chunk 92 optimal weight: 0.0570 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.0980 chunk 98 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 overall best weight: 0.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.146896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.091030 restraints weight = 23467.298| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.27 r_work: 0.3080 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12968 Z= 0.096 Angle : 0.509 8.272 18644 Z= 0.256 Chirality : 0.031 0.188 2285 Planarity : 0.004 0.035 1542 Dihedral : 23.265 179.051 4576 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.25 % Allowed : 8.13 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.29), residues: 924 helix: 1.70 (0.26), residues: 454 sheet: 0.16 (0.52), residues: 86 loop : -0.92 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 581 HIS 0.007 0.001 HIS A 779 PHE 0.009 0.001 PHE A 568 TYR 0.020 0.001 TYR A 168 ARG 0.007 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 556) hydrogen bonds : angle 3.88361 ( 1463) covalent geometry : bond 0.00191 (12968) covalent geometry : angle 0.50854 (18644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 1.322 Fit side-chains REVERT: A 372 MET cc_start: 0.4888 (mmp) cc_final: 0.4650 (mmm) REVERT: A 536 LEU cc_start: 0.9057 (tp) cc_final: 0.8733 (tp) REVERT: A 962 ARG cc_start: 0.8801 (pmt170) cc_final: 0.7453 (pmt170) REVERT: A 1059 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8332 (ttmm) outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.2698 time to fit residues: 17.4579 Evaluate side-chains 40 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 779 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 30.0000 chunk 68 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS A1085 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.143559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.087322 restraints weight = 22985.725| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.16 r_work: 0.3003 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12968 Z= 0.188 Angle : 0.562 8.345 18644 Z= 0.283 Chirality : 0.034 0.186 2285 Planarity : 0.004 0.034 1542 Dihedral : 23.225 178.239 4576 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.86 % Allowed : 8.50 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.29), residues: 924 helix: 1.62 (0.25), residues: 455 sheet: -0.01 (0.49), residues: 103 loop : -0.89 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 581 HIS 0.004 0.001 HIS A1075 PHE 0.021 0.002 PHE A 331 TYR 0.013 0.001 TYR A 168 ARG 0.008 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 556) hydrogen bonds : angle 3.92872 ( 1463) covalent geometry : bond 0.00422 (12968) covalent geometry : angle 0.56161 (18644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 1.185 Fit side-chains REVERT: A 372 MET cc_start: 0.4806 (mmp) cc_final: 0.4520 (mmm) REVERT: A 1059 LYS cc_start: 0.8764 (ttmt) cc_final: 0.8393 (ttmm) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.2672 time to fit residues: 17.5049 Evaluate side-chains 38 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 1016 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 49 optimal weight: 0.0870 chunk 100 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.145574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089160 restraints weight = 23228.082| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.25 r_work: 0.3045 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12968 Z= 0.102 Angle : 0.507 8.715 18644 Z= 0.255 Chirality : 0.031 0.188 2285 Planarity : 0.004 0.034 1542 Dihedral : 23.185 178.251 4576 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.62 % Allowed : 11.33 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.29), residues: 924 helix: 1.85 (0.26), residues: 455 sheet: 0.17 (0.50), residues: 96 loop : -0.84 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 581 HIS 0.006 0.001 HIS A 779 PHE 0.012 0.001 PHE A 331 TYR 0.014 0.001 TYR A 168 ARG 0.007 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 556) hydrogen bonds : angle 3.77159 ( 1463) covalent geometry : bond 0.00213 (12968) covalent geometry : angle 0.50748 (18644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 1.047 Fit side-chains REVERT: A 372 MET cc_start: 0.4768 (mmp) cc_final: 0.4493 (mmm) REVERT: A 1059 LYS cc_start: 0.8763 (ttmt) cc_final: 0.8386 (ttmm) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.2321 time to fit residues: 15.6131 Evaluate side-chains 39 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 1088 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 8 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.144626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.087974 restraints weight = 23548.337| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.25 r_work: 0.3019 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12968 Z= 0.143 Angle : 0.525 8.714 18644 Z= 0.264 Chirality : 0.032 0.192 2285 Planarity : 0.004 0.050 1542 Dihedral : 23.146 177.933 4576 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.11 % Allowed : 10.84 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.29), residues: 924 helix: 1.85 (0.25), residues: 454 sheet: 0.18 (0.50), residues: 96 loop : -0.86 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 581 HIS 0.006 0.001 HIS A 779 PHE 0.017 0.001 PHE A 331 TYR 0.011 0.001 TYR A 168 ARG 0.010 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 556) hydrogen bonds : angle 3.76539 ( 1463) covalent geometry : bond 0.00316 (12968) covalent geometry : angle 0.52539 (18644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 1.273 Fit side-chains REVERT: A 1059 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8447 (ttmm) outliers start: 9 outliers final: 7 residues processed: 42 average time/residue: 0.2607 time to fit residues: 18.3422 Evaluate side-chains 42 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1090 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 48 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.145275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088749 restraints weight = 23184.793| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.22 r_work: 0.3037 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12968 Z= 0.115 Angle : 0.512 8.834 18644 Z= 0.256 Chirality : 0.031 0.193 2285 Planarity : 0.004 0.034 1542 Dihedral : 23.117 177.862 4576 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.86 % Allowed : 11.45 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.29), residues: 924 helix: 1.93 (0.25), residues: 454 sheet: 0.24 (0.50), residues: 96 loop : -0.85 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 581 HIS 0.005 0.001 HIS A 779 PHE 0.014 0.001 PHE A 331 TYR 0.011 0.001 TYR A 168 ARG 0.009 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 556) hydrogen bonds : angle 3.70211 ( 1463) covalent geometry : bond 0.00248 (12968) covalent geometry : angle 0.51245 (18644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.981 Fit side-chains REVERT: A 1059 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8444 (ttmm) outliers start: 7 outliers final: 7 residues processed: 42 average time/residue: 0.1996 time to fit residues: 13.9502 Evaluate side-chains 42 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1090 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 48 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 0.0020 chunk 78 optimal weight: 0.0170 chunk 89 optimal weight: 0.4980 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 overall best weight: 0.2404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS A1085 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.147464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.091467 restraints weight = 23398.484| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.25 r_work: 0.3088 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12968 Z= 0.089 Angle : 0.489 8.927 18644 Z= 0.243 Chirality : 0.030 0.193 2285 Planarity : 0.004 0.034 1542 Dihedral : 23.029 177.849 4576 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.86 % Allowed : 11.95 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.29), residues: 924 helix: 2.11 (0.25), residues: 456 sheet: 0.24 (0.50), residues: 96 loop : -0.83 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 581 HIS 0.011 0.001 HIS A 779 PHE 0.008 0.001 PHE A 568 TYR 0.013 0.001 TYR A 168 ARG 0.007 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 556) hydrogen bonds : angle 3.56970 ( 1463) covalent geometry : bond 0.00179 (12968) covalent geometry : angle 0.48855 (18644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 1.042 Fit side-chains REVERT: A 372 MET cc_start: 0.4087 (mmm) cc_final: 0.3834 (mmm) REVERT: A 1059 LYS cc_start: 0.8797 (ttmt) cc_final: 0.8439 (ttmm) outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 0.2021 time to fit residues: 14.5687 Evaluate side-chains 44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1090 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 12 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.146992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.090823 restraints weight = 23148.998| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.24 r_work: 0.3080 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12968 Z= 0.098 Angle : 0.489 8.856 18644 Z= 0.243 Chirality : 0.030 0.196 2285 Planarity : 0.004 0.034 1542 Dihedral : 22.972 177.478 4576 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.74 % Allowed : 12.56 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.29), residues: 924 helix: 2.13 (0.25), residues: 458 sheet: 0.28 (0.53), residues: 86 loop : -0.77 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 581 HIS 0.004 0.001 HIS A 609 PHE 0.011 0.001 PHE A 331 TYR 0.010 0.001 TYR A 168 ARG 0.006 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 556) hydrogen bonds : angle 3.53956 ( 1463) covalent geometry : bond 0.00207 (12968) covalent geometry : angle 0.48855 (18644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.970 Fit side-chains REVERT: A 536 LEU cc_start: 0.9007 (tp) cc_final: 0.8749 (tp) REVERT: A 1059 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8540 (ttmm) outliers start: 6 outliers final: 6 residues processed: 42 average time/residue: 0.1973 time to fit residues: 13.8361 Evaluate side-chains 44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1090 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 31 optimal weight: 4.9990 chunk 74 optimal weight: 0.0970 chunk 98 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 84 optimal weight: 0.0010 chunk 16 optimal weight: 10.0000 chunk 103 optimal weight: 0.2980 chunk 9 optimal weight: 20.0000 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.147769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.094531 restraints weight = 23109.285| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.27 r_work: 0.3081 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12968 Z= 0.089 Angle : 0.483 8.897 18644 Z= 0.239 Chirality : 0.030 0.197 2285 Planarity : 0.004 0.031 1542 Dihedral : 22.940 177.359 4576 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.74 % Allowed : 13.05 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.29), residues: 924 helix: 2.25 (0.25), residues: 456 sheet: 0.30 (0.54), residues: 86 loop : -0.77 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 581 HIS 0.004 0.001 HIS A 779 PHE 0.009 0.001 PHE A 331 TYR 0.011 0.001 TYR A 168 ARG 0.006 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 556) hydrogen bonds : angle 3.49233 ( 1463) covalent geometry : bond 0.00184 (12968) covalent geometry : angle 0.48262 (18644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.957 Fit side-chains REVERT: A 941 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7489 (mt-10) REVERT: A 1054 MET cc_start: 0.7842 (ttm) cc_final: 0.7560 (ttm) REVERT: A 1059 LYS cc_start: 0.8919 (ttmt) cc_final: 0.8546 (ttmm) outliers start: 6 outliers final: 6 residues processed: 43 average time/residue: 0.2046 time to fit residues: 14.5491 Evaluate side-chains 44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1090 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 94 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.147087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.090808 restraints weight = 23197.931| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.26 r_work: 0.3073 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12968 Z= 0.103 Angle : 0.488 8.865 18644 Z= 0.242 Chirality : 0.030 0.199 2285 Planarity : 0.004 0.031 1542 Dihedral : 22.910 177.006 4576 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.86 % Allowed : 12.93 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.29), residues: 924 helix: 2.24 (0.25), residues: 457 sheet: 0.32 (0.54), residues: 86 loop : -0.77 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 581 HIS 0.008 0.001 HIS A 779 PHE 0.013 0.001 PHE A 331 TYR 0.009 0.001 TYR A 168 ARG 0.006 0.000 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 556) hydrogen bonds : angle 3.50805 ( 1463) covalent geometry : bond 0.00222 (12968) covalent geometry : angle 0.48849 (18644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6424.23 seconds wall clock time: 112 minutes 14.95 seconds (6734.95 seconds total)