Starting phenix.real_space_refine on Sun Dec 10 10:04:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6b_12737/12_2023/7o6b_12737.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6b_12737/12_2023/7o6b_12737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6b_12737/12_2023/7o6b_12737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6b_12737/12_2023/7o6b_12737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6b_12737/12_2023/7o6b_12737.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6b_12737/12_2023/7o6b_12737.pdb" } resolution = 3.88 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= -0.001 sd= 0.019 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 S 18 5.16 5 C 4543 2.51 5 N 1206 2.21 5 O 1393 1.98 5 H 7040 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 944": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14200 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 14200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 879, 14200 Classifications: {'peptide': 879} Link IDs: {'PTRANS': 35, 'TRANS': 843} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.62, per 1000 atoms: 0.54 Number of scatterers: 14200 At special positions: 0 Unit cell: (68.724, 120.888, 126.684, 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 18 16.00 O 1393 8.00 N 1206 7.00 C 4543 6.00 H 7040 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1152 " - pdb=" SG CYS A1160 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 11.53 Conformation dependent library (CDL) restraints added in 1.7 seconds 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 4 sheets defined 61.9% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 323 through 330 Processing helix chain 'A' and resid 340 through 360 Processing helix chain 'A' and resid 366 through 383 removed outlier: 3.809A pdb=" N PHE A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.762A pdb=" N SER A 400 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 442 removed outlier: 3.869A pdb=" N GLU A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 466 through 477 Processing helix chain 'A' and resid 510 through 516 removed outlier: 4.167A pdb=" N VAL A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.592A pdb=" N VAL A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 4.025A pdb=" N ASN A 554 " --> pdb=" O GLU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 removed outlier: 3.825A pdb=" N SER A 579 " --> pdb=" O GLN A 575 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU A 581 " --> pdb=" O TYR A 577 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 600 removed outlier: 3.972A pdb=" N LYS A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 622 removed outlier: 4.180A pdb=" N ASP A 622 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 637 through 650 removed outlier: 4.269A pdb=" N PHE A 641 " --> pdb=" O ASP A 637 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 642 " --> pdb=" O PRO A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 675 removed outlier: 3.637A pdb=" N LEU A 669 " --> pdb=" O TYR A 665 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE A 672 " --> pdb=" O HIS A 668 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 734 removed outlier: 3.838A pdb=" N GLN A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP A 704 " --> pdb=" O LYS A 700 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 807 removed outlier: 4.127A pdb=" N PHE A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 835 removed outlier: 3.941A pdb=" N LYS A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 860 Processing helix chain 'A' and resid 860 through 867 removed outlier: 3.573A pdb=" N ALA A 864 " --> pdb=" O SER A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 886 Processing helix chain 'A' and resid 886 through 894 Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 907 through 911 Processing helix chain 'A' and resid 912 through 931 removed outlier: 3.541A pdb=" N ALA A 923 " --> pdb=" O ALA A 919 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 939 Processing helix chain 'A' and resid 941 through 946 Processing helix chain 'A' and resid 947 through 951 Processing helix chain 'A' and resid 955 through 970 removed outlier: 3.713A pdb=" N ILE A 960 " --> pdb=" O LYS A 956 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP A 961 " --> pdb=" O ARG A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 986 through 994 Processing helix chain 'A' and resid 1014 through 1019 Processing helix chain 'A' and resid 1022 through 1024 No H-bonds generated for 'chain 'A' and resid 1022 through 1024' Processing helix chain 'A' and resid 1025 through 1037 Processing helix chain 'A' and resid 1040 through 1051 Processing helix chain 'A' and resid 1053 through 1063 removed outlier: 4.091A pdb=" N ILE A1057 " --> pdb=" O MET A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1071 Processing helix chain 'A' and resid 1074 through 1087 Processing helix chain 'A' and resid 1090 through 1101 Processing helix chain 'A' and resid 1117 through 1126 Processing helix chain 'A' and resid 1175 through 1179 removed outlier: 4.237A pdb=" N GLU A1178 " --> pdb=" O PRO A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1226 through 1240 removed outlier: 3.956A pdb=" N GLU A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A1236 " --> pdb=" O GLU A1232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 604 through 606 Processing sheet with id=AA2, first strand: chain 'A' and resid 776 through 782 removed outlier: 3.601A pdb=" N ARG A 778 " --> pdb=" O TYR A 769 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 766 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 812 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 811 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 933 through 934 removed outlier: 6.250A pdb=" N VAL A 933 " --> pdb=" O TYR A 998 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1136 through 1145 removed outlier: 6.857A pdb=" N ILE A1151 " --> pdb=" O GLU A1143 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU A1159 " --> pdb=" O ALA A1200 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL A1202 " --> pdb=" O GLU A1159 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL A1161 " --> pdb=" O VAL A1202 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR A1199 " --> pdb=" O ILE A1193 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE A1193 " --> pdb=" O THR A1199 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLU A1201 " --> pdb=" O ILE A1191 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A1186 " --> pdb=" O VAL A1140 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1050 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: 5.50 Time building geometry restraints manager: 11.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7036 1.03 - 1.23: 131 1.23 - 1.43: 2981 1.43 - 1.63: 4165 1.63 - 1.83: 30 Bond restraints: 14343 Sorted by residual: bond pdb=" NH1 ARG A1141 " pdb="HH12 ARG A1141 " ideal model delta sigma weight residual 0.860 0.830 0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" NH1 ARG A 957 " pdb="HH12 ARG A 957 " ideal model delta sigma weight residual 0.860 0.837 0.023 2.00e-02 2.50e+03 1.36e+00 bond pdb=" CG1 ILE A1044 " pdb=" CD1 ILE A1044 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.21e+00 bond pdb=" CG LEU A 642 " pdb=" CD2 LEU A 642 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.61e-01 bond pdb=" NH1 ARG A1066 " pdb="HH12 ARG A1066 " ideal model delta sigma weight residual 0.860 0.843 0.017 2.00e-02 2.50e+03 6.92e-01 ... (remaining 14338 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.35: 483 107.35 - 114.00: 16904 114.00 - 120.65: 4862 120.65 - 127.30: 3611 127.30 - 133.95: 70 Bond angle restraints: 25930 Sorted by residual: angle pdb=" N PRO A 541 " pdb=" CA PRO A 541 " pdb=" C PRO A 541 " ideal model delta sigma weight residual 112.47 121.12 -8.65 2.06e+00 2.36e-01 1.76e+01 angle pdb=" N SER A 542 " pdb=" CA SER A 542 " pdb=" C SER A 542 " ideal model delta sigma weight residual 114.12 119.78 -5.66 1.39e+00 5.18e-01 1.66e+01 angle pdb=" C SER A 542 " pdb=" N SER A 543 " pdb=" CA SER A 543 " ideal model delta sigma weight residual 122.33 117.20 5.13 1.68e+00 3.54e-01 9.31e+00 angle pdb=" N SER A 543 " pdb=" CA SER A 543 " pdb=" C SER A 543 " ideal model delta sigma weight residual 108.69 113.48 -4.79 1.77e+00 3.19e-01 7.33e+00 angle pdb=" N GLY A1117 " pdb=" CA GLY A1117 " pdb=" C GLY A1117 " ideal model delta sigma weight residual 113.18 119.18 -6.00 2.37e+00 1.78e-01 6.42e+00 ... (remaining 25925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6218 17.66 - 35.33: 328 35.33 - 52.99: 67 52.99 - 70.66: 16 70.66 - 88.32: 1 Dihedral angle restraints: 6630 sinusoidal: 3530 harmonic: 3100 Sorted by residual: dihedral pdb=" CB CYS A1152 " pdb=" SG CYS A1152 " pdb=" SG CYS A1160 " pdb=" CB CYS A1160 " ideal model delta sinusoidal sigma weight residual -86.00 -149.02 63.02 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CD ARG A1109 " pdb=" NE ARG A1109 " pdb=" CZ ARG A1109 " pdb=" NH1 ARG A1109 " ideal model delta sinusoidal sigma weight residual 0.00 32.83 -32.83 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CA ASP A 622 " pdb=" CB ASP A 622 " pdb=" CG ASP A 622 " pdb=" OD1 ASP A 622 " ideal model delta sinusoidal sigma weight residual -30.00 -85.26 55.26 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 6627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 865 0.047 - 0.093: 169 0.093 - 0.140: 47 0.140 - 0.186: 6 0.186 - 0.233: 1 Chirality restraints: 1088 Sorted by residual: chirality pdb=" CA PRO A 541 " pdb=" N PRO A 541 " pdb=" C PRO A 541 " pdb=" CB PRO A 541 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO A 818 " pdb=" N PRO A 818 " pdb=" C PRO A 818 " pdb=" CB PRO A 818 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE A 747 " pdb=" N ILE A 747 " pdb=" C ILE A 747 " pdb=" CB ILE A 747 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 1085 not shown) Planarity restraints: 2127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1141 " -0.060 9.50e-02 1.11e+02 6.21e-02 7.83e+01 pdb=" NE ARG A1141 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A1141 " -0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A1141 " -0.103 2.00e-02 2.50e+03 pdb=" NH2 ARG A1141 " 0.056 2.00e-02 2.50e+03 pdb="HH11 ARG A1141 " -0.007 2.00e-02 2.50e+03 pdb="HH12 ARG A1141 " 0.109 2.00e-02 2.50e+03 pdb="HH21 ARG A1141 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A1141 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 957 " 0.137 9.50e-02 1.11e+02 6.81e-02 5.95e+01 pdb=" NE ARG A 957 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 957 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG A 957 " -0.098 2.00e-02 2.50e+03 pdb=" NH2 ARG A 957 " 0.036 2.00e-02 2.50e+03 pdb="HH11 ARG A 957 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 957 " 0.097 2.00e-02 2.50e+03 pdb="HH21 ARG A 957 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 957 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1109 " -0.495 9.50e-02 1.11e+02 1.67e-01 4.54e+01 pdb=" NE ARG A1109 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG A1109 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG A1109 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A1109 " 0.040 2.00e-02 2.50e+03 pdb="HH11 ARG A1109 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A1109 " 0.032 2.00e-02 2.50e+03 pdb="HH21 ARG A1109 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A1109 " -0.042 2.00e-02 2.50e+03 ... (remaining 2124 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 219 2.04 - 2.68: 21803 2.68 - 3.32: 41829 3.32 - 3.96: 50574 3.96 - 4.60: 78866 Nonbonded interactions: 193291 Sorted by model distance: nonbonded pdb=" HG1 THR A 895 " pdb=" OE1 GLU A 898 " model vdw 1.401 1.850 nonbonded pdb=" OE2 GLU A 866 " pdb="HH22 ARG A 882 " model vdw 1.544 1.850 nonbonded pdb="HH11 ARG A 976 " pdb=" OH TYR A1026 " model vdw 1.573 1.850 nonbonded pdb=" O LYS A 749 " pdb=" H ASN A 809 " model vdw 1.584 1.850 nonbonded pdb=" H LEU A 974 " pdb=" OE1 GLN A 978 " model vdw 1.588 1.850 ... (remaining 193286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.210 Extract box with map and model: 4.380 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 49.830 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 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 : 0.003 0.043 7303 Z= 0.173 Angle : 0.672 8.647 9879 Z= 0.401 Chirality : 0.042 0.233 1088 Planarity : 0.012 0.206 1290 Dihedral : 11.536 88.323 2758 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.38 % Allowed : 3.41 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.27), residues: 865 helix: -0.17 (0.22), residues: 465 sheet: -1.36 (0.60), residues: 74 loop : -0.76 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.006 TRP A 415 HIS 0.016 0.004 HIS A 905 PHE 0.019 0.003 PHE A 407 TYR 0.028 0.006 TYR A 998 ARG 0.043 0.005 ARG A1109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 125 average time/residue: 0.5140 time to fit residues: 82.4685 Evaluate side-chains 76 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1616 time to fit residues: 1.7648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 26 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7303 Z= 0.222 Angle : 0.570 6.998 9879 Z= 0.317 Chirality : 0.040 0.144 1088 Planarity : 0.005 0.052 1290 Dihedral : 3.933 26.745 952 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.52 % Allowed : 7.95 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.29), residues: 865 helix: 0.51 (0.23), residues: 479 sheet: -0.97 (0.64), residues: 72 loop : -0.59 (0.38), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 918 HIS 0.006 0.001 HIS A1022 PHE 0.014 0.002 PHE A 424 TYR 0.012 0.001 TYR A 876 ARG 0.005 0.000 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 88 average time/residue: 0.4003 time to fit residues: 48.8859 Evaluate side-chains 88 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1677 time to fit residues: 4.6182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.4980 chunk 24 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7303 Z= 0.186 Angle : 0.521 6.864 9879 Z= 0.286 Chirality : 0.039 0.139 1088 Planarity : 0.004 0.047 1290 Dihedral : 3.997 26.578 952 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.25 % Allowed : 10.48 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.29), residues: 865 helix: 0.68 (0.23), residues: 482 sheet: -1.05 (0.64), residues: 72 loop : -0.55 (0.38), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1146 HIS 0.004 0.001 HIS A1022 PHE 0.015 0.002 PHE A 424 TYR 0.012 0.001 TYR A 876 ARG 0.003 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 81 average time/residue: 0.4055 time to fit residues: 45.1244 Evaluate side-chains 79 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1589 time to fit residues: 2.1653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7303 Z= 0.263 Angle : 0.568 6.823 9879 Z= 0.318 Chirality : 0.039 0.142 1088 Planarity : 0.004 0.048 1290 Dihedral : 4.340 25.390 952 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.02 % Allowed : 11.49 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.28), residues: 865 helix: 0.22 (0.23), residues: 487 sheet: -1.07 (0.65), residues: 69 loop : -0.97 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A1225 HIS 0.006 0.001 HIS A1022 PHE 0.021 0.002 PHE A 424 TYR 0.013 0.002 TYR A 883 ARG 0.005 0.001 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 83 average time/residue: 0.4272 time to fit residues: 49.1028 Evaluate side-chains 83 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1698 time to fit residues: 5.5544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 75 optimal weight: 0.0170 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7303 Z= 0.280 Angle : 0.588 6.845 9879 Z= 0.330 Chirality : 0.040 0.143 1088 Planarity : 0.004 0.044 1290 Dihedral : 4.524 24.048 952 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.63 % Allowed : 14.27 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.28), residues: 865 helix: -0.04 (0.23), residues: 481 sheet: -1.25 (0.63), residues: 69 loop : -1.28 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1225 HIS 0.005 0.001 HIS A1022 PHE 0.018 0.002 PHE A 424 TYR 0.022 0.002 TYR A 876 ARG 0.005 0.001 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 74 average time/residue: 0.4168 time to fit residues: 42.3524 Evaluate side-chains 72 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1784 time to fit residues: 3.0363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 0.0670 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7303 Z= 0.149 Angle : 0.497 6.887 9879 Z= 0.267 Chirality : 0.039 0.143 1088 Planarity : 0.004 0.041 1290 Dihedral : 4.185 21.772 952 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.63 % Allowed : 14.77 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.29), residues: 865 helix: 0.76 (0.23), residues: 476 sheet: -1.08 (0.64), residues: 69 loop : -0.71 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 350 HIS 0.003 0.001 HIS A 905 PHE 0.015 0.001 PHE A 437 TYR 0.014 0.001 TYR A 876 ARG 0.003 0.000 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 81 average time/residue: 0.4438 time to fit residues: 48.7057 Evaluate side-chains 77 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1606 time to fit residues: 2.6776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 33 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7303 Z= 0.171 Angle : 0.508 8.706 9879 Z= 0.274 Chirality : 0.038 0.138 1088 Planarity : 0.004 0.041 1290 Dihedral : 4.145 20.388 952 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.25 % Allowed : 15.91 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 865 helix: 0.81 (0.24), residues: 480 sheet: -0.87 (0.62), residues: 70 loop : -0.74 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 415 HIS 0.003 0.001 HIS A1022 PHE 0.013 0.001 PHE A 641 TYR 0.013 0.001 TYR A 876 ARG 0.014 0.000 ARG A1067 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 73 average time/residue: 0.4390 time to fit residues: 43.9783 Evaluate side-chains 73 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1750 time to fit residues: 2.2758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7303 Z= 0.149 Angle : 0.487 7.634 9879 Z= 0.262 Chirality : 0.038 0.139 1088 Planarity : 0.004 0.038 1290 Dihedral : 4.063 18.730 952 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.63 % Allowed : 15.66 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.29), residues: 865 helix: 1.03 (0.24), residues: 475 sheet: -0.86 (0.62), residues: 70 loop : -0.57 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 415 HIS 0.003 0.001 HIS A 905 PHE 0.011 0.001 PHE A 641 TYR 0.013 0.001 TYR A 891 ARG 0.008 0.000 ARG A1067 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 75 average time/residue: 0.4383 time to fit residues: 44.8288 Evaluate side-chains 76 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.199 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2589 time to fit residues: 3.5087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 9.9990 chunk 61 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7303 Z= 0.141 Angle : 0.487 9.491 9879 Z= 0.257 Chirality : 0.038 0.140 1088 Planarity : 0.003 0.040 1290 Dihedral : 3.963 18.162 952 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.13 % Allowed : 16.16 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.30), residues: 865 helix: 1.18 (0.24), residues: 475 sheet: -0.83 (0.63), residues: 70 loop : -0.45 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 415 HIS 0.003 0.001 HIS A 633 PHE 0.011 0.001 PHE A 437 TYR 0.012 0.001 TYR A 891 ARG 0.005 0.000 ARG A1067 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.4510 time to fit residues: 44.3819 Evaluate side-chains 70 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7303 Z= 0.224 Angle : 0.535 8.884 9879 Z= 0.293 Chirality : 0.039 0.156 1088 Planarity : 0.004 0.043 1290 Dihedral : 4.160 18.175 952 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.38 % Allowed : 15.66 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.29), residues: 865 helix: 0.81 (0.24), residues: 480 sheet: -0.90 (0.63), residues: 70 loop : -0.70 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 918 HIS 0.005 0.001 HIS A1022 PHE 0.015 0.002 PHE A 424 TYR 0.011 0.001 TYR A 883 ARG 0.005 0.001 ARG A1067 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 427 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue ILE 701 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 62 average time/residue: 0.4291 time to fit residues: 37.0403 Evaluate side-chains 63 residues out of total 795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1619 time to fit residues: 2.0672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.0010 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.131405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.104595 restraints weight = 80349.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.108176 restraints weight = 40340.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.110295 restraints weight = 26325.694| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7303 Z= 0.145 Angle : 0.491 8.726 9879 Z= 0.262 Chirality : 0.038 0.139 1088 Planarity : 0.004 0.040 1290 Dihedral : 4.033 18.541 952 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.13 % Allowed : 16.16 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.30), residues: 865 helix: 1.15 (0.24), residues: 475 sheet: -0.84 (0.63), residues: 70 loop : -0.52 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 415 HIS 0.005 0.001 HIS A 633 PHE 0.011 0.001 PHE A 437 TYR 0.011 0.001 TYR A 891 ARG 0.004 0.000 ARG A1067 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3034.30 seconds wall clock time: 58 minutes 30.79 seconds (3510.79 seconds total)