Starting phenix.real_space_refine on Sun Sep 29 05:54:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgx_14714/09_2024/7zgx_14714.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgx_14714/09_2024/7zgx_14714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgx_14714/09_2024/7zgx_14714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgx_14714/09_2024/7zgx_14714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgx_14714/09_2024/7zgx_14714.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgx_14714/09_2024/7zgx_14714.cif" } resolution = 2.88 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= 0.002 sd= 0.047 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 18 5.16 5 C 13245 2.51 5 N 3795 2.21 5 O 4293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21351 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 12.99, per 1000 atoms: 0.61 Number of scatterers: 21351 At special positions: 0 Unit cell: (164.418, 155.42, 129.244, 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 18 16.00 O 4293 8.00 N 3795 7.00 C 13245 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: 4.84 Conformation dependent library (CDL) restraints added in 2.6 seconds 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 26 sheets defined 7.0% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 221 through 252 removed outlier: 3.575A pdb=" N THR A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.888A pdb=" N PHE A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.731A pdb=" N THR A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 594 removed outlier: 4.161A pdb=" N ALA A 594 " --> pdb=" O MET A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 875 removed outlier: 4.242A pdb=" N GLY A 875 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 924 Processing helix chain 'B' and resid 221 through 252 removed outlier: 3.650A pdb=" N THR B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.852A pdb=" N PHE B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 451 through 456 removed outlier: 3.613A pdb=" N THR B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 594 removed outlier: 4.223A pdb=" N ALA B 594 " --> pdb=" O MET B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 787 Processing helix chain 'B' and resid 870 through 875 removed outlier: 4.283A pdb=" N GLY B 875 " --> pdb=" O LEU B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 924 Processing helix chain 'C' and resid 221 through 252 removed outlier: 3.540A pdb=" N GLU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 removed outlier: 3.982A pdb=" N PHE C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.550A pdb=" N THR C 455 " --> pdb=" O THR C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 4.132A pdb=" N ALA C 594 " --> pdb=" O MET C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 870 through 875 removed outlier: 3.620A pdb=" N GLY C 873 " --> pdb=" O GLY C 870 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY C 875 " --> pdb=" O LEU C 872 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 269 removed outlier: 3.743A pdb=" N SER A 383 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER A 267 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLU A 381 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR A 269 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR A 379 " --> pdb=" O THR A 269 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 379 through 393 current: chain 'A' and resid 418 through 420 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 418 through 420 current: chain 'A' and resid 473 through 483 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 473 through 483 current: chain 'A' and resid 756 through 765 removed outlier: 3.799A pdb=" N PHE A 758 " --> pdb=" O THR A 777 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 789 through 792 current: chain 'A' and resid 803 through 814 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 932 through 936 current: chain 'A' and resid 977 through 984 removed outlier: 3.500A pdb=" N ALA A1016 " --> pdb=" O SER A 998 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1057 through 1061 current: chain 'A' and resid 1075 through 1085 removed outlier: 3.831A pdb=" N GLY A1115 " --> pdb=" O ASP A1081 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A1133 " --> pdb=" O ASN A1114 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1125 through 1134 current: chain 'B' and resid 379 through 393 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 379 through 393 current: chain 'B' and resid 418 through 420 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 418 through 420 current: chain 'B' and resid 473 through 483 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 473 through 483 current: chain 'B' and resid 982 through 984 removed outlier: 3.558A pdb=" N ALA B1016 " --> pdb=" O SER B 998 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1014 through 1022 current: chain 'B' and resid 1054 through 1061 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1054 through 1061 current: chain 'B' and resid 1076 through 1085 removed outlier: 3.584A pdb=" N GLY B1115 " --> pdb=" O ASP B1081 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B1133 " --> pdb=" O ASN B1114 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1126 through 1134 current: chain 'C' and resid 379 through 394 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 379 through 394 current: chain 'C' and resid 418 through 420 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 418 through 420 current: chain 'C' and resid 982 through 984 removed outlier: 3.725A pdb=" N ALA C1016 " --> pdb=" O SER C 998 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY C1063 " --> pdb=" O ASN C1036 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C1080 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY C1115 " --> pdb=" O ASP C1081 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C1133 " --> pdb=" O ASN C1114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 334 through 337 Processing sheet with id=AA3, first strand: chain 'A' and resid 436 through 438 Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AA5, first strand: chain 'A' and resid 487 through 490 removed outlier: 5.817A pdb=" N VAL A 562 " --> pdb=" O ARG A 549 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 611 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER A 622 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 650 through 651 removed outlier: 3.858A pdb=" N THR A 650 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 724 through 729 removed outlier: 6.165A pdb=" N LEU A 724 " --> pdb=" O ILE A 753 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 821 Processing sheet with id=AA9, first strand: chain 'A' and resid 962 through 963 removed outlier: 3.564A pdb=" N ASP A 972 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1088 through 1091 Processing sheet with id=AB2, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AB3, first strand: chain 'B' and resid 465 through 467 Processing sheet with id=AB4, first strand: chain 'B' and resid 487 through 490 removed outlier: 5.848A pdb=" N VAL B 562 " --> pdb=" O ARG B 549 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 609 " --> pdb=" O TYR B 624 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B 622 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.981A pdb=" N THR B 650 " --> pdb=" O ASP B 658 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 672 through 683 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 672 through 683 current: chain 'B' and resid 748 through 765 removed outlier: 3.557A pdb=" N PHE B 758 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR B 774 " --> pdb=" O GLY B 793 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 793 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 792 " --> pdb=" O THR B 811 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 819 through 821 Processing sheet with id=AB8, first strand: chain 'B' and resid 962 through 963 Processing sheet with id=AB9, first strand: chain 'B' and resid 1088 through 1091 Processing sheet with id=AC1, first strand: chain 'C' and resid 334 through 337 Processing sheet with id=AC2, first strand: chain 'C' and resid 487 through 490 removed outlier: 5.734A pdb=" N VAL C 562 " --> pdb=" O ARG C 549 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 611 " --> pdb=" O SER C 622 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER C 622 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 650 through 651 removed outlier: 3.837A pdb=" N THR C 650 " --> pdb=" O ASP C 658 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 674 through 681 removed outlier: 6.373A pdb=" N LYS C 761 " --> pdb=" O TYR C 676 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU C 678 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY C 759 " --> pdb=" O LEU C 678 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR C 680 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY C 757 " --> pdb=" O TYR C 680 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 758 " --> pdb=" O THR C 777 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET C 789 " --> pdb=" O SER C 778 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 789 through 792 current: chain 'C' and resid 803 through 814 removed outlier: 6.449A pdb=" N VAL C 962 " --> pdb=" O PHE C 973 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N PHE C 973 " --> pdb=" O VAL C 962 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 724 through 726 removed outlier: 6.069A pdb=" N LEU C 724 " --> pdb=" O ILE C 753 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 819 through 821 Processing sheet with id=AC7, first strand: chain 'C' and resid 880 through 881 removed outlier: 3.687A pdb=" N ARG C 891 " --> pdb=" O SER C 880 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1088 through 1091 596 hydrogen bonds defined for protein. 1575 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: 8.35 Time building geometry restraints manager: 5.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7370 1.34 - 1.46: 4133 1.46 - 1.57: 10241 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 21774 Sorted by residual: bond pdb=" C PHE B 881 " pdb=" N GLU B 882 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.46e-02 4.69e+03 4.16e+00 bond pdb=" C TYR C1090 " pdb=" N THR C1091 " ideal model delta sigma weight residual 1.332 1.309 0.023 1.44e-02 4.82e+03 2.65e+00 bond pdb=" C TYR A1090 " pdb=" N THR A1091 " ideal model delta sigma weight residual 1.333 1.310 0.024 1.61e-02 3.86e+03 2.18e+00 bond pdb=" C THR B 439 " pdb=" N ASN B 440 " ideal model delta sigma weight residual 1.334 1.313 0.022 1.52e-02 4.33e+03 2.04e+00 bond pdb=" CA GLY B 387 " pdb=" C GLY B 387 " ideal model delta sigma weight residual 1.520 1.510 0.010 7.30e-03 1.88e+04 2.03e+00 ... (remaining 21769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 28771 2.07 - 4.13: 751 4.13 - 6.20: 61 6.20 - 8.26: 11 8.26 - 10.33: 1 Bond angle restraints: 29595 Sorted by residual: angle pdb=" C ASN C 632 " pdb=" CA ASN C 632 " pdb=" CB ASN C 632 " ideal model delta sigma weight residual 116.54 109.34 7.20 1.15e+00 7.56e-01 3.92e+01 angle pdb=" C THR B 597 " pdb=" CA THR B 597 " pdb=" CB THR B 597 " ideal model delta sigma weight residual 116.54 110.29 6.25 1.15e+00 7.56e-01 2.95e+01 angle pdb=" C THR C 597 " pdb=" CA THR C 597 " pdb=" CB THR C 597 " ideal model delta sigma weight residual 116.54 110.39 6.15 1.15e+00 7.56e-01 2.86e+01 angle pdb=" C THR A 597 " pdb=" CA THR A 597 " pdb=" CB THR A 597 " ideal model delta sigma weight residual 116.54 110.41 6.13 1.15e+00 7.56e-01 2.85e+01 angle pdb=" N VAL C 990 " pdb=" CA VAL C 990 " pdb=" C VAL C 990 " ideal model delta sigma weight residual 113.22 106.77 6.45 1.23e+00 6.61e-01 2.75e+01 ... (remaining 29590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11623 17.76 - 35.52: 781 35.52 - 53.28: 109 53.28 - 71.05: 20 71.05 - 88.81: 13 Dihedral angle restraints: 12546 sinusoidal: 4599 harmonic: 7947 Sorted by residual: dihedral pdb=" CA TYR C 696 " pdb=" C TYR C 696 " pdb=" N GLY C 697 " pdb=" CA GLY C 697 " ideal model delta harmonic sigma weight residual 180.00 149.82 30.18 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA TYR A 696 " pdb=" C TYR A 696 " pdb=" N GLY A 697 " pdb=" CA GLY A 697 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA GLN B1086 " pdb=" C GLN B1086 " pdb=" N ASN B1087 " pdb=" CA ASN B1087 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 12543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2094 0.041 - 0.083: 813 0.083 - 0.124: 258 0.124 - 0.165: 33 0.165 - 0.206: 6 Chirality restraints: 3204 Sorted by residual: chirality pdb=" CB ILE B 535 " pdb=" CA ILE B 535 " pdb=" CG1 ILE B 535 " pdb=" CG2 ILE B 535 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE A 262 " pdb=" CA ILE A 262 " pdb=" CG1 ILE A 262 " pdb=" CG2 ILE A 262 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CB ILE C 262 " pdb=" CA ILE C 262 " pdb=" CG1 ILE C 262 " pdb=" CG2 ILE C 262 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 3201 not shown) Planarity restraints: 4017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 512 " -0.028 2.00e-02 2.50e+03 2.05e-02 7.37e+00 pdb=" CG PHE A 512 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 512 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 512 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 512 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 512 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 512 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 512 " 0.026 2.00e-02 2.50e+03 1.94e-02 6.60e+00 pdb=" CG PHE B 512 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 512 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 512 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 512 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 512 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 512 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 468 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO C 469 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 469 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 469 " -0.035 5.00e-02 4.00e+02 ... (remaining 4014 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 982 2.71 - 3.26: 21430 3.26 - 3.80: 33614 3.80 - 4.35: 43816 4.35 - 4.90: 76532 Nonbonded interactions: 176374 Sorted by model distance: nonbonded pdb=" OH TYR B1117 " pdb=" OE1 GLU B1119 " model vdw 2.159 3.040 nonbonded pdb=" OD1 ASP B 307 " pdb=" OH TYR B1090 " model vdw 2.172 3.040 nonbonded pdb=" OD1 ASN A 733 " pdb=" N ASN A 734 " model vdw 2.179 3.120 nonbonded pdb=" OD1 ASP C 307 " pdb=" OH TYR C1090 " model vdw 2.208 3.040 nonbonded pdb=" O ARG B 251 " pdb=" OG SER B 395 " model vdw 2.212 3.040 ... (remaining 176369 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' selection = chain 'C' } 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: 9.610 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: 0.940 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 47.620 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 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:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 : 0.005 0.045 21774 Z= 0.356 Angle : 0.767 10.330 29595 Z= 0.466 Chirality : 0.048 0.206 3204 Planarity : 0.005 0.062 4017 Dihedral : 12.229 88.806 7614 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.30 % Favored : 88.28 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.11 (0.15), residues: 2841 helix: -1.25 (0.37), residues: 147 sheet: -1.69 (0.15), residues: 1212 loop : -2.48 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 538 HIS 0.004 0.001 HIS B 612 PHE 0.045 0.002 PHE A 512 TYR 0.020 0.002 TYR C 890 ARG 0.006 0.001 ARG C 816 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.288 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8328 (t70) cc_final: 0.7994 (t0) REVERT: A 831 ASP cc_start: 0.8144 (p0) cc_final: 0.7907 (p0) REVERT: B 250 GLU cc_start: 0.8218 (pt0) cc_final: 0.7840 (tm-30) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 1.0274 time to fit residues: 90.7937 Evaluate side-chains 44 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 221 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN A 503 GLN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 GLN A 818 GLN B 493 ASN B 570 GLN C 810 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21774 Z= 0.307 Angle : 0.626 7.707 29595 Z= 0.340 Chirality : 0.047 0.171 3204 Planarity : 0.004 0.056 4017 Dihedral : 5.156 28.046 3189 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.16 % Favored : 88.49 % Rotamer: Outliers : 0.51 % Allowed : 5.83 % Favored : 93.66 % 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: -2.95 (0.15), residues: 2841 helix: -0.81 (0.38), residues: 147 sheet: -1.64 (0.15), residues: 1173 loop : -2.34 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 538 HIS 0.004 0.001 HIS B 621 PHE 0.025 0.002 PHE A 512 TYR 0.016 0.001 TYR A 837 ARG 0.005 0.001 ARG B 806 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 2.468 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8370 (t70) cc_final: 0.7975 (t0) REVERT: A 831 ASP cc_start: 0.8190 (p0) cc_final: 0.7902 (p0) REVERT: B 250 GLU cc_start: 0.8173 (pt0) cc_final: 0.7952 (tm-30) outliers start: 11 outliers final: 5 residues processed: 63 average time/residue: 1.0119 time to fit residues: 78.1635 Evaluate side-chains 51 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 590 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 GLN A 818 GLN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 21774 Z= 0.443 Angle : 0.660 7.910 29595 Z= 0.359 Chirality : 0.049 0.193 3204 Planarity : 0.005 0.061 4017 Dihedral : 5.249 29.324 3189 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.76 % Favored : 87.89 % Rotamer: Outliers : 1.65 % Allowed : 8.08 % Favored : 90.27 % 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: -2.96 (0.15), residues: 2841 helix: -1.11 (0.36), residues: 165 sheet: -1.60 (0.15), residues: 1170 loop : -2.37 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 538 HIS 0.004 0.002 HIS A 612 PHE 0.026 0.002 PHE A 512 TYR 0.017 0.002 TYR A 837 ARG 0.005 0.001 ARG C1022 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 47 time to evaluate : 2.426 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8532 (t70) cc_final: 0.8096 (t0) REVERT: A 831 ASP cc_start: 0.8193 (p0) cc_final: 0.7912 (p0) REVERT: C 422 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8292 (t70) outliers start: 36 outliers final: 16 residues processed: 77 average time/residue: 0.7702 time to fit residues: 76.5332 Evaluate side-chains 59 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 866 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 0.9980 chunk 192 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 122 optimal weight: 0.0670 chunk 172 optimal weight: 5.9990 chunk 257 optimal weight: 0.0980 chunk 272 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 244 optimal weight: 0.0370 chunk 73 optimal weight: 0.1980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN A 707 GLN A 818 GLN B 570 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21774 Z= 0.128 Angle : 0.547 7.060 29595 Z= 0.295 Chirality : 0.044 0.164 3204 Planarity : 0.004 0.052 4017 Dihedral : 4.730 22.921 3189 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.08 % Favored : 90.60 % Rotamer: Outliers : 0.96 % Allowed : 10.10 % Favored : 88.93 % 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: -2.60 (0.15), residues: 2841 helix: -0.35 (0.40), residues: 147 sheet: -1.32 (0.15), residues: 1155 loop : -2.21 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 538 HIS 0.002 0.001 HIS A 621 PHE 0.019 0.001 PHE A 512 TYR 0.011 0.001 TYR C 698 ARG 0.004 0.000 ARG C1022 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 64 time to evaluate : 2.549 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8406 (t70) cc_final: 0.7940 (t0) REVERT: A 586 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: A 831 ASP cc_start: 0.8118 (p0) cc_final: 0.7878 (p0) REVERT: B 565 ARG cc_start: 0.6352 (mtt180) cc_final: 0.4935 (mtm180) REVERT: C 422 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8239 (t70) REVERT: C 1022 ARG cc_start: 0.7005 (mtp-110) cc_final: 0.6625 (mtm180) outliers start: 21 outliers final: 11 residues processed: 82 average time/residue: 0.8287 time to fit residues: 85.6472 Evaluate side-chains 62 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 866 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 202 optimal weight: 0.0470 chunk 112 optimal weight: 7.9990 chunk 232 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 GLN A 818 GLN B 493 ASN B 570 GLN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 21774 Z= 0.404 Angle : 0.631 8.111 29595 Z= 0.341 Chirality : 0.047 0.161 3204 Planarity : 0.004 0.058 4017 Dihedral : 4.965 26.284 3189 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.51 % Favored : 88.24 % Rotamer: Outliers : 1.97 % Allowed : 11.16 % Favored : 86.87 % 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: -2.75 (0.15), residues: 2841 helix: -1.30 (0.34), residues: 186 sheet: -1.43 (0.15), residues: 1179 loop : -2.22 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 538 HIS 0.004 0.002 HIS B 621 PHE 0.032 0.002 PHE C 512 TYR 0.016 0.002 TYR A 837 ARG 0.004 0.001 ARG C 681 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 45 time to evaluate : 2.180 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8595 (t70) cc_final: 0.8099 (OUTLIER) REVERT: A 586 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: A 590 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7399 (ppp) REVERT: A 831 ASP cc_start: 0.8136 (p0) cc_final: 0.7875 (p0) REVERT: A 1139 LEU cc_start: 0.8049 (mt) cc_final: 0.7822 (mp) REVERT: C 422 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8289 (t70) REVERT: C 865 SER cc_start: 0.8483 (m) cc_final: 0.8094 (t) REVERT: C 1022 ARG cc_start: 0.7232 (mtp-110) cc_final: 0.7018 (ttp-110) outliers start: 43 outliers final: 27 residues processed: 82 average time/residue: 0.7442 time to fit residues: 78.7163 Evaluate side-chains 74 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 45 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 866 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 160 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21774 Z= 0.189 Angle : 0.557 8.782 29595 Z= 0.301 Chirality : 0.045 0.154 3204 Planarity : 0.004 0.055 4017 Dihedral : 4.752 24.800 3189 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.54 % Favored : 90.18 % Rotamer: Outliers : 2.07 % Allowed : 11.85 % Favored : 86.09 % 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: -2.61 (0.15), residues: 2841 helix: -1.15 (0.35), residues: 186 sheet: -1.32 (0.15), residues: 1173 loop : -2.16 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 538 HIS 0.002 0.001 HIS C 582 PHE 0.029 0.001 PHE C 512 TYR 0.012 0.001 TYR A 837 ARG 0.002 0.000 ARG C1088 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 50 time to evaluate : 2.576 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8505 (t70) cc_final: 0.8008 (OUTLIER) REVERT: A 586 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: A 590 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7367 (ppp) REVERT: A 800 TYR cc_start: 0.7535 (t80) cc_final: 0.7325 (t80) REVERT: A 831 ASP cc_start: 0.8125 (p0) cc_final: 0.7849 (p0) REVERT: A 1139 LEU cc_start: 0.8057 (mt) cc_final: 0.7799 (mp) REVERT: B 565 ARG cc_start: 0.6212 (mtt180) cc_final: 0.5103 (mtm180) REVERT: C 422 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8258 (t70) REVERT: C 865 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8023 (t) REVERT: C 1022 ARG cc_start: 0.7078 (mtp-110) cc_final: 0.6664 (mtm180) outliers start: 45 outliers final: 28 residues processed: 88 average time/residue: 0.7510 time to fit residues: 85.1428 Evaluate side-chains 79 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 48 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 866 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 271 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.099 21774 Z= 0.646 Angle : 0.749 12.917 29595 Z= 0.404 Chirality : 0.052 0.194 3204 Planarity : 0.005 0.064 4017 Dihedral : 5.367 29.884 3189 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.02 % Favored : 86.66 % Rotamer: Outliers : 2.48 % Allowed : 11.71 % Favored : 85.81 % 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: -2.87 (0.15), residues: 2841 helix: -1.46 (0.33), residues: 186 sheet: -1.52 (0.15), residues: 1182 loop : -2.29 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 538 HIS 0.006 0.002 HIS B 621 PHE 0.034 0.002 PHE C 512 TYR 0.020 0.002 TYR A 837 ARG 0.006 0.001 ARG C 681 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 47 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8724 (t70) cc_final: 0.8236 (t70) REVERT: A 586 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: A 590 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7386 (ppp) REVERT: A 665 LYS cc_start: 0.5282 (pptt) cc_final: 0.4625 (pptt) REVERT: B 250 GLU cc_start: 0.8249 (pt0) cc_final: 0.8030 (tm-30) REVERT: C 422 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8333 (t70) REVERT: C 789 MET cc_start: 0.8707 (tpp) cc_final: 0.7662 (ttm) REVERT: C 865 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8130 (t) outliers start: 54 outliers final: 35 residues processed: 95 average time/residue: 0.7456 time to fit residues: 90.4824 Evaluate side-chains 85 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 46 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 914 VAL Chi-restraints excluded: chain C residue 1029 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 213 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C1087 ASN C1114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21774 Z= 0.184 Angle : 0.576 12.843 29595 Z= 0.309 Chirality : 0.045 0.159 3204 Planarity : 0.004 0.059 4017 Dihedral : 4.897 26.538 3189 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.68 % Favored : 90.04 % Rotamer: Outliers : 2.11 % Allowed : 12.26 % Favored : 85.63 % 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: -2.61 (0.15), residues: 2841 helix: -1.12 (0.35), residues: 186 sheet: -1.32 (0.16), residues: 1173 loop : -2.15 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 538 HIS 0.002 0.001 HIS A 939 PHE 0.028 0.001 PHE C 512 TYR 0.013 0.001 TYR C 698 ARG 0.007 0.000 ARG C1022 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 48 time to evaluate : 2.270 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8593 (t70) cc_final: 0.8071 (OUTLIER) REVERT: A 800 TYR cc_start: 0.7354 (t80) cc_final: 0.6868 (t80) REVERT: C 422 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8282 (t70) REVERT: C 789 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8318 (ttt) REVERT: C 865 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.7966 (t) outliers start: 46 outliers final: 30 residues processed: 87 average time/residue: 0.6681 time to fit residues: 76.1982 Evaluate side-chains 75 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 43 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 789 MET Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1029 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 0.3980 chunk 260 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 253 optimal weight: 0.4980 chunk 152 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21774 Z= 0.198 Angle : 0.560 14.073 29595 Z= 0.299 Chirality : 0.045 0.152 3204 Planarity : 0.004 0.058 4017 Dihedral : 4.669 25.416 3189 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.67 % Favored : 89.16 % Rotamer: Outliers : 1.74 % Allowed : 12.72 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.44 (0.16), residues: 2841 helix: -0.93 (0.36), residues: 183 sheet: -1.19 (0.16), residues: 1170 loop : -2.07 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 538 HIS 0.003 0.001 HIS C 582 PHE 0.028 0.001 PHE C 512 TYR 0.012 0.001 TYR A 837 ARG 0.006 0.000 ARG C1022 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 45 time to evaluate : 2.273 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8592 (t70) cc_final: 0.8091 (OUTLIER) REVERT: A 423 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8995 (tt) REVERT: A 800 TYR cc_start: 0.7360 (t80) cc_final: 0.6906 (t80) REVERT: B 739 ASP cc_start: 0.8083 (m-30) cc_final: 0.7872 (m-30) REVERT: C 422 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8285 (t70) outliers start: 38 outliers final: 30 residues processed: 78 average time/residue: 0.7582 time to fit residues: 76.4527 Evaluate side-chains 73 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 42 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1029 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 163 optimal weight: 0.0670 chunk 127 optimal weight: 5.9990 chunk 186 optimal weight: 0.0770 chunk 280 optimal weight: 0.0000 chunk 258 optimal weight: 0.0060 chunk 223 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 overall best weight: 0.1096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 GLN ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN C 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21774 Z= 0.121 Angle : 0.530 14.771 29595 Z= 0.282 Chirality : 0.044 0.142 3204 Planarity : 0.004 0.055 4017 Dihedral : 4.334 21.617 3189 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.73 % Favored : 91.09 % Rotamer: Outliers : 1.29 % Allowed : 13.31 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.18 (0.16), residues: 2841 helix: -0.35 (0.40), residues: 165 sheet: -0.96 (0.16), residues: 1131 loop : -1.98 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 538 HIS 0.003 0.001 HIS C 612 PHE 0.025 0.001 PHE A 666 TYR 0.014 0.001 TYR C1042 ARG 0.006 0.000 ARG C1022 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 64 time to evaluate : 2.474 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8410 (t70) cc_final: 0.7974 (OUTLIER) REVERT: A 800 TYR cc_start: 0.7311 (t80) cc_final: 0.6880 (t80) REVERT: A 1002 THR cc_start: 0.9087 (m) cc_final: 0.8848 (t) REVERT: A 1139 LEU cc_start: 0.7961 (mt) cc_final: 0.7739 (mp) REVERT: B 565 ARG cc_start: 0.6147 (mtt180) cc_final: 0.5126 (mtm180) REVERT: B 880 SER cc_start: 0.8850 (t) cc_final: 0.8346 (p) REVERT: C 356 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7652 (p) REVERT: C 624 TYR cc_start: 0.8161 (t80) cc_final: 0.7773 (t80) outliers start: 28 outliers final: 22 residues processed: 88 average time/residue: 0.7319 time to fit residues: 84.4841 Evaluate side-chains 71 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 49 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1029 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 0.0040 chunk 224 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 GLN ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN C 400 GLN C 420 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.073449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061380 restraints weight = 53933.323| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.82 r_work: 0.3045 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21774 Z= 0.236 Angle : 0.558 13.546 29595 Z= 0.298 Chirality : 0.045 0.198 3204 Planarity : 0.004 0.058 4017 Dihedral : 4.447 23.995 3189 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.07 % Favored : 89.79 % Rotamer: Outliers : 1.47 % Allowed : 13.36 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.14 (0.16), residues: 2841 helix: -0.49 (0.39), residues: 165 sheet: -0.98 (0.16), residues: 1167 loop : -1.89 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 538 HIS 0.003 0.001 HIS C 582 PHE 0.027 0.001 PHE C 512 TYR 0.013 0.001 TYR A 837 ARG 0.007 0.000 ARG B1022 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4130.11 seconds wall clock time: 75 minutes 13.19 seconds (4513.19 seconds total)