Starting phenix.real_space_refine on Sat Nov 16 23:23:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9z_36120/11_2024/8j9z_36120.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9z_36120/11_2024/8j9z_36120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9z_36120/11_2024/8j9z_36120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9z_36120/11_2024/8j9z_36120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9z_36120/11_2024/8j9z_36120.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9z_36120/11_2024/8j9z_36120.cif" } resolution = 3.13 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= 0.046 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 7818 2.51 5 N 2086 2.21 5 O 2200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12154 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6077 Classifications: {'peptide': 747} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 716} Chain breaks: 1 Chain: "B" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6077 Classifications: {'peptide': 747} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 716} Chain breaks: 1 Time building chain proxies: 7.29, per 1000 atoms: 0.60 Number of scatterers: 12154 At special positions: 0 Unit cell: (124.45, 116.85, 114, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2200 8.00 N 2086 7.00 C 7818 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: 3.06 Conformation dependent library (CDL) restraints added in 1.7 seconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 16 sheets defined 52.7% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.859A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.904A pdb=" N HIS A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.617A pdb=" N HIS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.566A pdb=" N ARG A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 687 through 705 removed outlier: 3.820A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 754 through 767 Processing helix chain 'A' and resid 806 through 814 removed outlier: 4.215A pdb=" N THR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.627A pdb=" N TRP A 820 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 877 Processing helix chain 'A' and resid 882 through 893 Processing helix chain 'A' and resid 942 through 952 Processing helix chain 'A' and resid 953 through 959 removed outlier: 4.114A pdb=" N PHE A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 990 Processing helix chain 'A' and resid 997 through 1004 Processing helix chain 'A' and resid 1027 through 1075 removed outlier: 3.623A pdb=" N ILE A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 4.828A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1079 Processing helix chain 'A' and resid 1081 through 1093 removed outlier: 3.626A pdb=" N ALA A1085 " --> pdb=" O ASP A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1117 Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.793A pdb=" N LEU A1126 " --> pdb=" O TYR A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1133 Processing helix chain 'A' and resid 1134 through 1160 removed outlier: 3.536A pdb=" N GLN A1160 " --> pdb=" O GLU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1187 Processing helix chain 'B' and resid 428 through 431 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 522 through 527 Processing helix chain 'B' and resid 547 through 560 Processing helix chain 'B' and resid 560 through 567 removed outlier: 3.859A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.904A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.616A pdb=" N HIS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 656 through 664 removed outlier: 3.566A pdb=" N ARG B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 687 through 705 removed outlier: 3.820A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 754 through 767 Processing helix chain 'B' and resid 806 through 814 removed outlier: 4.216A pdb=" N THR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 821 removed outlier: 3.626A pdb=" N TRP B 820 " --> pdb=" O GLU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 877 Processing helix chain 'B' and resid 882 through 893 Processing helix chain 'B' and resid 942 through 952 Processing helix chain 'B' and resid 953 through 959 removed outlier: 4.113A pdb=" N PHE B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 990 Processing helix chain 'B' and resid 997 through 1004 Processing helix chain 'B' and resid 1027 through 1075 removed outlier: 3.623A pdb=" N ILE B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 4.829A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1079 Processing helix chain 'B' and resid 1081 through 1093 removed outlier: 3.625A pdb=" N ALA B1085 " --> pdb=" O ASP B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1104 Processing helix chain 'B' and resid 1109 through 1117 Processing helix chain 'B' and resid 1122 through 1127 removed outlier: 3.793A pdb=" N LEU B1126 " --> pdb=" O TYR B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1133 Processing helix chain 'B' and resid 1134 through 1160 removed outlier: 3.536A pdb=" N GLN B1160 " --> pdb=" O GLU B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1187 Processing sheet with id=AA1, first strand: chain 'A' and resid 418 through 419 removed outlier: 5.392A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE A 685 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR A 638 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.752A pdb=" N VAL A 825 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AA6, first strand: chain 'A' and resid 909 through 913 Processing sheet with id=AA7, first strand: chain 'A' and resid 922 through 925 removed outlier: 6.010A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1013 through 1016 removed outlier: 4.503A pdb=" N LEU A1013 " --> pdb=" O PHE A1025 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 418 through 419 removed outlier: 5.392A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE B 685 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR B 638 " --> pdb=" O ILE B 685 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AB2, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AB3, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.752A pdb=" N VAL B 825 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 849 through 850 Processing sheet with id=AB5, first strand: chain 'B' and resid 909 through 913 Processing sheet with id=AB6, first strand: chain 'B' and resid 922 through 925 removed outlier: 6.011A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1013 through 1016 removed outlier: 4.503A pdb=" N LEU B1013 " --> pdb=" O PHE B1025 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1728 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: 4.05 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3916 1.34 - 1.46: 2499 1.46 - 1.58: 5953 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 12446 Sorted by residual: bond pdb=" CB PRO A1096 " pdb=" CG PRO A1096 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.67e+00 bond pdb=" CB PRO B1096 " pdb=" CG PRO B1096 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.62e+00 bond pdb=" CB GLU A 524 " pdb=" CG GLU A 524 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.11e-01 bond pdb=" CB GLU B 524 " pdb=" CG GLU B 524 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.84e-01 bond pdb=" CA LEU A1036 " pdb=" C LEU A1036 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.26e-01 ... (remaining 12441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 16452 1.10 - 2.19: 257 2.19 - 3.29: 87 3.29 - 4.39: 13 4.39 - 5.48: 7 Bond angle restraints: 16816 Sorted by residual: angle pdb=" CA GLU B 524 " pdb=" CB GLU B 524 " pdb=" CG GLU B 524 " ideal model delta sigma weight residual 114.10 118.92 -4.82 2.00e+00 2.50e-01 5.82e+00 angle pdb=" CA GLU A 524 " pdb=" CB GLU A 524 " pdb=" CG GLU A 524 " ideal model delta sigma weight residual 114.10 118.90 -4.80 2.00e+00 2.50e-01 5.75e+00 angle pdb=" CB GLU A 524 " pdb=" CG GLU A 524 " pdb=" CD GLU A 524 " ideal model delta sigma weight residual 112.60 116.21 -3.61 1.70e+00 3.46e-01 4.51e+00 angle pdb=" CB GLU B 524 " pdb=" CG GLU B 524 " pdb=" CD GLU B 524 " ideal model delta sigma weight residual 112.60 116.19 -3.59 1.70e+00 3.46e-01 4.45e+00 angle pdb=" CA PRO A1096 " pdb=" N PRO A1096 " pdb=" CD PRO A1096 " ideal model delta sigma weight residual 112.00 109.52 2.48 1.40e+00 5.10e-01 3.15e+00 ... (remaining 16811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 6476 17.85 - 35.71: 732 35.71 - 53.56: 222 53.56 - 71.42: 26 71.42 - 89.27: 18 Dihedral angle restraints: 7474 sinusoidal: 3088 harmonic: 4386 Sorted by residual: dihedral pdb=" CB GLU B 658 " pdb=" CG GLU B 658 " pdb=" CD GLU B 658 " pdb=" OE1 GLU B 658 " ideal model delta sinusoidal sigma weight residual 0.00 89.19 -89.19 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 658 " pdb=" CG GLU A 658 " pdb=" CD GLU A 658 " pdb=" OE1 GLU A 658 " ideal model delta sinusoidal sigma weight residual 0.00 89.17 -89.17 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU B 970 " pdb=" CG GLU B 970 " pdb=" CD GLU B 970 " pdb=" OE1 GLU B 970 " ideal model delta sinusoidal sigma weight residual 0.00 -88.51 88.51 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 7471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1105 0.026 - 0.053: 463 0.053 - 0.079: 158 0.079 - 0.105: 65 0.105 - 0.132: 29 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CA ILE B 707 " pdb=" N ILE B 707 " pdb=" C ILE B 707 " pdb=" CB ILE B 707 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE A 707 " pdb=" N ILE A 707 " pdb=" C ILE A 707 " pdb=" CB ILE A 707 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE A 780 " pdb=" N ILE A 780 " pdb=" C ILE A 780 " pdb=" CB ILE A 780 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1817 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 669 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.05e+01 pdb=" N PRO A 670 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 669 " -0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO B 670 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 670 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 670 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 524 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" CD GLU B 524 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU B 524 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 524 " 0.010 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 349 2.72 - 3.27: 11554 3.27 - 3.81: 19877 3.81 - 4.36: 24111 4.36 - 4.90: 42538 Nonbonded interactions: 98429 Sorted by model distance: nonbonded pdb=" NH2 ARG B1049 " pdb=" O PRO B1105 " model vdw 2.177 3.120 nonbonded pdb=" NH2 ARG A1049 " pdb=" O PRO A1105 " model vdw 2.177 3.120 nonbonded pdb=" O VAL B 838 " pdb=" NH1 ARG B1039 " model vdw 2.250 3.120 nonbonded pdb=" O VAL A 838 " pdb=" NH1 ARG A1039 " model vdw 2.251 3.120 nonbonded pdb=" OD2 ASP A 818 " pdb=" NH2 ARG A1039 " model vdw 2.254 3.120 ... (remaining 98424 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 29.490 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 : 0.002 0.082 12446 Z= 0.147 Angle : 0.411 5.482 16816 Z= 0.220 Chirality : 0.037 0.132 1820 Planarity : 0.004 0.081 2142 Dihedral : 16.682 89.271 4662 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.15 % Allowed : 18.02 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.31 (0.23), residues: 1486 helix: 2.22 (0.20), residues: 704 sheet: -1.16 (0.34), residues: 230 loop : 0.11 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1189 HIS 0.002 0.000 HIS B 883 PHE 0.010 0.001 PHE A 649 TYR 0.012 0.001 TYR A 888 ARG 0.008 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 1.532 Fit side-chains REVERT: A 856 TRP cc_start: 0.7409 (m100) cc_final: 0.7134 (m100) REVERT: B 503 LYS cc_start: 0.7053 (tppt) cc_final: 0.6495 (ttmm) REVERT: B 701 ASP cc_start: 0.8363 (t70) cc_final: 0.8125 (t0) outliers start: 2 outliers final: 0 residues processed: 146 average time/residue: 0.2704 time to fit residues: 56.7848 Evaluate side-chains 133 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 38 optimal weight: 0.0000 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 chunk 116 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS B 903 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12446 Z= 0.158 Angle : 0.422 5.628 16816 Z= 0.222 Chirality : 0.038 0.136 1820 Planarity : 0.004 0.061 2142 Dihedral : 3.229 12.710 1662 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.45 % Allowed : 17.94 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.30 (0.23), residues: 1486 helix: 2.17 (0.20), residues: 706 sheet: -1.05 (0.35), residues: 224 loop : 0.10 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1189 HIS 0.002 0.000 HIS A 566 PHE 0.009 0.001 PHE B 596 TYR 0.016 0.001 TYR B 888 ARG 0.005 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: B 542 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.6848 (pp) REVERT: B 735 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: B 790 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8482 (mp) REVERT: B 825 VAL cc_start: 0.8541 (p) cc_final: 0.8304 (m) REVERT: B 878 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7996 (ptpp) REVERT: B 1048 MET cc_start: 0.8606 (mtp) cc_final: 0.8231 (mmm) outliers start: 19 outliers final: 8 residues processed: 150 average time/residue: 0.2858 time to fit residues: 62.4119 Evaluate side-chains 140 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 1119 GLN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1119 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 0.3980 chunk 119 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS B 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12446 Z= 0.204 Angle : 0.432 5.585 16816 Z= 0.227 Chirality : 0.039 0.134 1820 Planarity : 0.003 0.050 2142 Dihedral : 3.330 13.533 1662 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.14 % Allowed : 17.25 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.26 (0.23), residues: 1486 helix: 2.09 (0.20), residues: 708 sheet: -0.96 (0.36), residues: 212 loop : 0.04 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1189 HIS 0.003 0.001 HIS A 789 PHE 0.009 0.001 PHE A 739 TYR 0.016 0.001 TYR A 888 ARG 0.007 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.368 Fit side-chains revert: symmetry clash REVERT: B 542 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.6888 (pp) REVERT: B 878 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8038 (ptpp) REVERT: B 1048 MET cc_start: 0.8569 (mtp) cc_final: 0.8185 (mtp) outliers start: 28 outliers final: 16 residues processed: 156 average time/residue: 0.2503 time to fit residues: 57.5571 Evaluate side-chains 149 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1119 GLN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1119 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 0.0010 chunk 64 optimal weight: 10.0000 chunk 90 optimal weight: 0.0970 chunk 135 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 38 optimal weight: 0.0970 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS B1010 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12446 Z= 0.132 Angle : 0.400 6.002 16816 Z= 0.210 Chirality : 0.037 0.130 1820 Planarity : 0.003 0.044 2142 Dihedral : 3.210 12.662 1662 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.14 % Allowed : 17.56 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.36 (0.23), residues: 1486 helix: 2.18 (0.20), residues: 708 sheet: -0.94 (0.37), residues: 212 loop : 0.10 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1189 HIS 0.003 0.000 HIS A 883 PHE 0.008 0.001 PHE A 710 TYR 0.016 0.001 TYR A 888 ARG 0.007 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: A 736 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.6942 (mtm180) REVERT: B 524 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7462 (tm-30) REVERT: B 542 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.6964 (pp) REVERT: B 584 LYS cc_start: 0.7689 (ttmt) cc_final: 0.7474 (ttpt) REVERT: B 825 VAL cc_start: 0.8707 (p) cc_final: 0.8423 (m) REVERT: B 878 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7997 (ptpp) REVERT: B 892 HIS cc_start: 0.6680 (m-70) cc_final: 0.6429 (m170) REVERT: B 1048 MET cc_start: 0.8547 (mtp) cc_final: 0.8179 (mtp) outliers start: 28 outliers final: 17 residues processed: 154 average time/residue: 0.2721 time to fit residues: 60.3671 Evaluate side-chains 146 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1119 GLN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1119 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12446 Z= 0.197 Angle : 0.425 5.493 16816 Z= 0.222 Chirality : 0.038 0.136 1820 Planarity : 0.003 0.041 2142 Dihedral : 3.334 13.655 1662 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.90 % Allowed : 17.25 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.32 (0.23), residues: 1486 helix: 2.16 (0.20), residues: 708 sheet: -0.92 (0.37), residues: 212 loop : 0.04 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1189 HIS 0.003 0.001 HIS B 789 PHE 0.008 0.001 PHE B 739 TYR 0.008 0.001 TYR B 946 ARG 0.006 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 1.412 Fit side-chains REVERT: A 524 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7440 (tm-30) REVERT: A 892 HIS cc_start: 0.6587 (m-70) cc_final: 0.6303 (m170) REVERT: B 521 LYS cc_start: 0.8717 (ttmt) cc_final: 0.8298 (ttmm) REVERT: B 524 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7506 (tm-30) REVERT: B 542 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7180 (pp) REVERT: B 701 ASP cc_start: 0.8153 (t70) cc_final: 0.7866 (t0) REVERT: B 736 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7008 (mtm180) REVERT: B 878 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8115 (ptpp) REVERT: B 892 HIS cc_start: 0.6702 (m-70) cc_final: 0.6388 (m170) REVERT: B 962 GLU cc_start: 0.7754 (tt0) cc_final: 0.7510 (tt0) REVERT: B 1048 MET cc_start: 0.8560 (mtp) cc_final: 0.8231 (mtp) outliers start: 38 outliers final: 26 residues processed: 166 average time/residue: 0.2591 time to fit residues: 62.5644 Evaluate side-chains 160 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1119 GLN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 736 ARG Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1119 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 880 ASN B1010 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12446 Z= 0.190 Angle : 0.430 6.951 16816 Z= 0.224 Chirality : 0.038 0.139 1820 Planarity : 0.003 0.040 2142 Dihedral : 3.349 13.677 1662 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.90 % Allowed : 17.33 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.32 (0.23), residues: 1486 helix: 2.18 (0.20), residues: 706 sheet: -0.96 (0.37), residues: 212 loop : 0.04 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1189 HIS 0.003 0.001 HIS A 789 PHE 0.008 0.001 PHE A 710 TYR 0.010 0.001 TYR A 946 ARG 0.008 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 1.484 Fit side-chains REVERT: A 441 SER cc_start: 0.8379 (OUTLIER) cc_final: 0.8051 (p) REVERT: A 524 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 892 HIS cc_start: 0.6671 (m-70) cc_final: 0.6359 (m170) REVERT: A 1156 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7340 (tp30) REVERT: B 521 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8448 (ttmm) REVERT: B 524 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7515 (tm-30) REVERT: B 542 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7319 (pp) REVERT: B 701 ASP cc_start: 0.8151 (t70) cc_final: 0.7856 (t0) REVERT: B 736 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.6987 (mtm180) REVERT: B 878 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8081 (ptpp) REVERT: B 892 HIS cc_start: 0.6619 (m-70) cc_final: 0.6225 (m170) REVERT: B 927 GLU cc_start: 0.7873 (tp30) cc_final: 0.7452 (mm-30) REVERT: B 962 GLU cc_start: 0.7724 (tt0) cc_final: 0.7462 (tt0) REVERT: B 1048 MET cc_start: 0.8564 (mtp) cc_final: 0.8241 (mtp) outliers start: 38 outliers final: 22 residues processed: 159 average time/residue: 0.2544 time to fit residues: 59.3211 Evaluate side-chains 155 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 736 ARG Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1119 GLN Chi-restraints excluded: chain B residue 1148 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 880 ASN B1010 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 12446 Z= 0.494 Angle : 0.563 8.021 16816 Z= 0.295 Chirality : 0.044 0.157 1820 Planarity : 0.004 0.039 2142 Dihedral : 3.883 16.579 1662 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.21 % Allowed : 17.10 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.74 (0.22), residues: 1486 helix: 1.68 (0.19), residues: 716 sheet: -0.96 (0.37), residues: 192 loop : -0.42 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B1189 HIS 0.006 0.001 HIS A 789 PHE 0.017 0.002 PHE B1191 TYR 0.016 0.002 TYR A1043 ARG 0.006 0.001 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 1.464 Fit side-chains REVERT: A 524 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 565 ILE cc_start: 0.9173 (mt) cc_final: 0.8953 (mp) REVERT: A 682 VAL cc_start: 0.8110 (m) cc_final: 0.7762 (p) REVERT: A 892 HIS cc_start: 0.6706 (m-70) cc_final: 0.6375 (m170) REVERT: A 1156 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7456 (tp30) REVERT: B 521 LYS cc_start: 0.8704 (ttmt) cc_final: 0.8384 (ttmm) REVERT: B 524 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 682 VAL cc_start: 0.8253 (m) cc_final: 0.7885 (p) REVERT: B 701 ASP cc_start: 0.8259 (t70) cc_final: 0.7903 (t0) REVERT: B 878 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8150 (ptpp) REVERT: B 927 GLU cc_start: 0.7903 (tp30) cc_final: 0.7597 (mm-30) REVERT: B 1156 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7407 (tp30) outliers start: 42 outliers final: 30 residues processed: 161 average time/residue: 0.2343 time to fit residues: 55.9736 Evaluate side-chains 153 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1058 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1119 GLN Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12446 Z= 0.186 Angle : 0.444 6.813 16816 Z= 0.231 Chirality : 0.038 0.137 1820 Planarity : 0.003 0.038 2142 Dihedral : 3.552 14.404 1662 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.83 % Allowed : 18.93 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.04 (0.23), residues: 1486 helix: 1.98 (0.20), residues: 706 sheet: -1.31 (0.34), residues: 218 loop : -0.02 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1189 HIS 0.002 0.000 HIS A 789 PHE 0.015 0.001 PHE A1002 TYR 0.010 0.001 TYR B 946 ARG 0.009 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.459 Fit side-chains REVERT: A 441 SER cc_start: 0.8403 (OUTLIER) cc_final: 0.8059 (p) REVERT: A 524 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7533 (tm-30) REVERT: B 441 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8032 (p) REVERT: B 524 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7634 (tm-30) REVERT: B 682 VAL cc_start: 0.8037 (m) cc_final: 0.7707 (p) REVERT: B 701 ASP cc_start: 0.8206 (t70) cc_final: 0.7874 (t0) REVERT: B 878 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8097 (ptpp) REVERT: B 1048 MET cc_start: 0.8633 (mtp) cc_final: 0.8272 (mtt) outliers start: 24 outliers final: 18 residues processed: 142 average time/residue: 0.2474 time to fit residues: 51.9111 Evaluate side-chains 144 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1148 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 57 optimal weight: 0.0470 chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12446 Z= 0.189 Angle : 0.434 6.789 16816 Z= 0.228 Chirality : 0.038 0.140 1820 Planarity : 0.003 0.037 2142 Dihedral : 3.473 14.661 1662 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.91 % Allowed : 18.70 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.11 (0.23), residues: 1486 helix: 2.05 (0.20), residues: 706 sheet: -1.31 (0.34), residues: 218 loop : 0.01 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1189 HIS 0.003 0.001 HIS B 789 PHE 0.013 0.001 PHE A1002 TYR 0.015 0.001 TYR A 555 ARG 0.008 0.000 ARG A 912 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 441 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8074 (p) REVERT: A 524 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7566 (tm-30) REVERT: A 1156 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: B 441 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.8091 (p) REVERT: B 521 LYS cc_start: 0.8710 (ttmt) cc_final: 0.8439 (ttmm) REVERT: B 524 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 682 VAL cc_start: 0.8089 (m) cc_final: 0.7752 (p) REVERT: B 701 ASP cc_start: 0.8217 (t70) cc_final: 0.7916 (t0) REVERT: B 878 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8109 (ptpp) REVERT: B 1048 MET cc_start: 0.8627 (mtp) cc_final: 0.8279 (mtt) outliers start: 25 outliers final: 17 residues processed: 143 average time/residue: 0.2505 time to fit residues: 52.5138 Evaluate side-chains 143 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1148 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 : 0.003 0.038 12446 Z= 0.204 Angle : 0.445 6.908 16816 Z= 0.231 Chirality : 0.039 0.140 1820 Planarity : 0.004 0.037 2142 Dihedral : 3.473 13.826 1662 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.83 % Allowed : 18.78 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.10 (0.23), residues: 1486 helix: 2.02 (0.20), residues: 708 sheet: -1.32 (0.34), residues: 218 loop : 0.03 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1189 HIS 0.003 0.001 HIS B 789 PHE 0.013 0.001 PHE A1002 TYR 0.015 0.001 TYR A 555 ARG 0.008 0.000 ARG B 912 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.453 Fit side-chains revert: symmetry clash REVERT: A 441 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.8079 (p) REVERT: A 524 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 1156 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: B 441 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.8074 (p) REVERT: B 521 LYS cc_start: 0.8707 (ttmt) cc_final: 0.8439 (ttmm) REVERT: B 524 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7673 (tm-30) REVERT: B 701 ASP cc_start: 0.8220 (t70) cc_final: 0.7913 (t0) REVERT: B 878 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8118 (ptpp) REVERT: B 1048 MET cc_start: 0.8629 (mtp) cc_final: 0.8274 (mtt) outliers start: 24 outliers final: 20 residues processed: 142 average time/residue: 0.2477 time to fit residues: 52.0079 Evaluate side-chains 143 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1148 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 0.0870 chunk 17 optimal weight: 0.4980 chunk 32 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 0.0570 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.179769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136649 restraints weight = 13012.906| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.16 r_work: 0.3347 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12446 Z= 0.135 Angle : 0.411 6.686 16816 Z= 0.215 Chirality : 0.037 0.134 1820 Planarity : 0.003 0.038 2142 Dihedral : 3.300 13.612 1662 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.76 % Allowed : 19.01 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.30 (0.23), residues: 1486 helix: 2.17 (0.20), residues: 708 sheet: -1.24 (0.34), residues: 218 loop : 0.15 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1189 HIS 0.003 0.000 HIS B 883 PHE 0.013 0.001 PHE A1002 TYR 0.013 0.001 TYR A 555 ARG 0.009 0.000 ARG B 912 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.10 seconds wall clock time: 48 minutes 53.62 seconds (2933.62 seconds total)