Starting phenix.real_space_refine on Sat Apr 6 08:27:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9r_36996/04_2024/8k9r_36996_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9r_36996/04_2024/8k9r_36996.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9r_36996/04_2024/8k9r_36996_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9r_36996/04_2024/8k9r_36996_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9r_36996/04_2024/8k9r_36996_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9r_36996/04_2024/8k9r_36996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9r_36996/04_2024/8k9r_36996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9r_36996/04_2024/8k9r_36996_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9r_36996/04_2024/8k9r_36996_neut_updated.pdb" } resolution = 2.68 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= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 33 5.16 5 C 4991 2.51 5 N 1271 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A ARG 757": "NH1" <-> "NH2" Residue "A PHE 826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1107": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7684 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7487 Classifications: {'peptide': 958} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 896} Chain breaks: 3 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 155 Unusual residues: {'05E': 1, 'CLR': 1, 'L9H': 1, 'MAN': 2, 'PA1': 1, 'PLM': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'80Y': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.91, per 1000 atoms: 0.64 Number of scatterers: 7684 At special positions: 0 Unit cell: (78.288, 91.336, 133.276, 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 33 16.00 P 3 15.00 O 1386 8.00 N 1271 7.00 C 4991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 449 " distance=2.04 Simple disulfide: pdb=" SG CYS A 574 " - pdb=" SG CYS A 606 " distance=2.03 Simple disulfide: pdb=" SG CYS A 729 " - pdb=" SG CYS A 793 " distance=2.04 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.5 seconds 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 5 sheets defined 42.1% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 147 through 169 removed outlier: 3.582A pdb=" N VAL A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.745A pdb=" N SER A 201 " --> pdb=" O ARG A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 234 through 250 removed outlier: 3.819A pdb=" N VAL A 237 " --> pdb=" O TYR A 234 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.618A pdb=" N GLU A 243 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR A 247 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A 248 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 282 through 304 removed outlier: 3.772A pdb=" N TYR A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 366 through 383 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 412 through 415 Processing helix chain 'A' and resid 445 through 448 No H-bonds generated for 'chain 'A' and resid 445 through 448' Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 475 through 486 Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 645 through 648 No H-bonds generated for 'chain 'A' and resid 645 through 648' Processing helix chain 'A' and resid 675 through 678 No H-bonds generated for 'chain 'A' and resid 675 through 678' Processing helix chain 'A' and resid 686 through 692 Processing helix chain 'A' and resid 778 through 780 No H-bonds generated for 'chain 'A' and resid 778 through 780' Processing helix chain 'A' and resid 791 through 793 No H-bonds generated for 'chain 'A' and resid 791 through 793' Processing helix chain 'A' and resid 805 through 821 removed outlier: 4.074A pdb=" N LEU A 812 " --> pdb=" O SER A 808 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TYR A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N MET A 814 " --> pdb=" O GLY A 810 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THR A 818 " --> pdb=" O MET A 814 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA A 821 " --> pdb=" O ARG A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 842 removed outlier: 3.645A pdb=" N VAL A 828 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 829 " --> pdb=" O PHE A 826 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 832 " --> pdb=" O SER A 829 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 835 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 838 " --> pdb=" O GLN A 835 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 842 " --> pdb=" O TYR A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 857 removed outlier: 3.673A pdb=" N ARG A 857 " --> pdb=" O ASP A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 871 Processing helix chain 'A' and resid 909 through 953 removed outlier: 4.430A pdb=" N PHE A 913 " --> pdb=" O PHE A 910 " (cutoff:3.500A) Proline residue: A 916 - end of helix removed outlier: 3.890A pdb=" N ARG A 953 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 992 removed outlier: 3.740A pdb=" N VAL A 990 " --> pdb=" O LEU A 986 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 992 " --> pdb=" O PHE A 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 986 through 992' Processing helix chain 'A' and resid 996 through 1021 Processing helix chain 'A' and resid 1024 through 1060 removed outlier: 3.540A pdb=" N ILE A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) Proline residue: A1045 - end of helix Proline residue: A1049 - end of helix removed outlier: 3.504A pdb=" N VAL A1053 " --> pdb=" O PRO A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1086 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1103 through 1124 removed outlier: 3.678A pdb=" N THR A1110 " --> pdb=" O LEU A1106 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A1111 " --> pdb=" O ARG A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1148 removed outlier: 3.568A pdb=" N LEU A1132 " --> pdb=" O ALA A1129 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS A1133 " --> pdb=" O TYR A1130 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 186 through 188 removed outlier: 4.949A pdb=" N PHE A 268 " --> pdb=" O TYR A 208 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 271 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 322 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE A 227 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 324 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN A 348 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL A 323 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE A 350 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY A 325 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR A 352 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR A 397 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N THR A 352 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 399 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 427 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 591 through 594 Processing sheet with id= C, first strand: chain 'A' and resid 523 through 525 Processing sheet with id= D, first strand: chain 'A' and resid 679 through 681 removed outlier: 8.372A pdb=" N HIS A 680 " --> pdb=" O MET A 705 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLU A 707 " --> pdb=" O HIS A 680 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU A 749 " --> pdb=" O LEU A 744 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 694 through 696 removed outlier: 4.577A pdb=" N ALA A 719 " --> pdb=" O ASP A 804 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 720 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: 2.83 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1171 1.30 - 1.43: 2107 1.43 - 1.56: 4545 1.56 - 1.69: 6 1.69 - 1.82: 55 Bond restraints: 7884 Sorted by residual: bond pdb=" O84 05E A1503 " pdb=" P83 05E A1503 " ideal model delta sigma weight residual 1.678 1.579 0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" OA5 L9H A1505 " pdb=" PA6 L9H A1505 " ideal model delta sigma weight residual 1.659 1.566 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C LYS A 235 " pdb=" O LYS A 235 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.38e-02 5.25e+03 2.14e+01 bond pdb=" C80 05E A1503 " pdb=" O97 05E A1503 " ideal model delta sigma weight residual 1.503 1.412 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" O75 80Y B 101 " pdb=" P76 80Y B 101 " ideal model delta sigma weight residual 1.646 1.559 0.087 2.00e-02 2.50e+03 1.89e+01 ... (remaining 7879 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.53: 238 105.53 - 112.68: 4318 112.68 - 119.82: 2556 119.82 - 126.96: 3528 126.96 - 134.11: 118 Bond angle restraints: 10758 Sorted by residual: angle pdb=" N THR B 2 " pdb=" CA THR B 2 " pdb=" C THR B 2 " ideal model delta sigma weight residual 114.56 106.82 7.74 1.27e+00 6.20e-01 3.72e+01 angle pdb=" N LYS A 235 " pdb=" CA LYS A 235 " pdb=" C LYS A 235 " ideal model delta sigma weight residual 113.17 106.37 6.80 1.26e+00 6.30e-01 2.92e+01 angle pdb=" C THR B 2 " pdb=" CA THR B 2 " pdb=" CB THR B 2 " ideal model delta sigma weight residual 109.13 115.48 -6.35 1.56e+00 4.11e-01 1.66e+01 angle pdb=" N PRO A 703 " pdb=" CA PRO A 703 " pdb=" C PRO A 703 " ideal model delta sigma weight residual 111.22 105.77 5.45 1.40e+00 5.10e-01 1.51e+01 angle pdb=" CA LEU A 902 " pdb=" C LEU A 902 " pdb=" O LEU A 902 " ideal model delta sigma weight residual 121.11 116.87 4.24 1.13e+00 7.83e-01 1.41e+01 ... (remaining 10753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 4679 35.73 - 71.46: 105 71.46 - 107.19: 11 107.19 - 142.91: 6 142.91 - 178.64: 1 Dihedral angle restraints: 4802 sinusoidal: 1980 harmonic: 2822 Sorted by residual: dihedral pdb=" C73 80Y B 101 " pdb=" C74 80Y B 101 " pdb=" O75 80Y B 101 " pdb=" P76 80Y B 101 " ideal model delta sinusoidal sigma weight residual 94.72 -86.64 -178.64 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB3 L9H A1505 " pdb=" CB1 L9H A1505 " pdb=" CB2 L9H A1505 " pdb=" OB0 L9H A1505 " ideal model delta sinusoidal sigma weight residual 255.68 125.62 130.06 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C2 MAN A1501 " pdb=" C1 MAN A1501 " pdb=" O5 MAN A1501 " pdb=" C5 MAN A1501 " ideal model delta sinusoidal sigma weight residual -57.62 62.32 -119.94 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 4799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.994: 1269 0.994 - 1.988: 0 1.988 - 2.981: 0 2.981 - 3.975: 0 3.975 - 4.969: 1 Chirality restraints: 1270 Sorted by residual: chirality pdb=" C5 L9H A1505 " pdb=" C2 L9H A1505 " pdb=" C7 L9H A1505 " pdb=" O6 L9H A1505 " both_signs ideal model delta sigma weight residual False -2.51 2.46 -4.97 2.00e-01 2.50e+01 6.17e+02 chirality pdb=" C2 MAN A1502 " pdb=" C1 MAN A1502 " pdb=" C3 MAN A1502 " pdb=" O2 MAN A1502 " both_signs ideal model delta sigma weight residual False 2.52 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE A 577 " pdb=" N ILE A 577 " pdb=" C ILE A 577 " pdb=" CB ILE A 577 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1267 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 379 " -0.027 2.00e-02 2.50e+03 2.46e-02 1.51e+01 pdb=" CG TRP A 379 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP A 379 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 379 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 379 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 379 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 379 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 379 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 379 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 379 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1135 " 0.016 2.00e-02 2.50e+03 2.01e-02 7.04e+00 pdb=" CG PHE A1135 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A1135 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A1135 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A1135 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A1135 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A1135 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 234 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.13e+00 pdb=" C TYR A 234 " 0.039 2.00e-02 2.50e+03 pdb=" O TYR A 234 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A 235 " -0.013 2.00e-02 2.50e+03 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1463 2.77 - 3.30: 7260 3.30 - 3.83: 13122 3.83 - 4.37: 16339 4.37 - 4.90: 27360 Nonbonded interactions: 65544 Sorted by model distance: nonbonded pdb=" NH2 ARG A 178 " pdb=" OE2 GLU A 634 " model vdw 2.233 2.520 nonbonded pdb=" O ASP A 901 " pdb=" OG SER A1127 " model vdw 2.281 2.440 nonbonded pdb=" NH1 ARG A 741 " pdb=" OE1 GLN A 786 " model vdw 2.310 2.520 nonbonded pdb=" NH1 ARG A 522 " pdb=" OE2 GLU A 671 " model vdw 2.353 2.520 nonbonded pdb=" OG SER A 716 " pdb=" NH2 ARG A 815 " model vdw 2.381 2.520 ... (remaining 65539 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.000 Extract box with map and model: 4.540 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.210 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.009 0.099 7884 Z= 0.615 Angle : 0.866 10.340 10758 Z= 0.503 Chirality : 0.149 4.969 1270 Planarity : 0.005 0.053 1330 Dihedral : 16.106 178.643 2961 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.33 % Allowed : 1.09 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.54 (0.27), residues: 952 helix: 0.78 (0.26), residues: 372 sheet: 1.26 (0.45), residues: 141 loop : -0.22 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP A 379 HIS 0.007 0.001 HIS A 281 PHE 0.045 0.002 PHE A1135 TYR 0.014 0.002 TYR A 372 ARG 0.007 0.001 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.916 Fit side-chains REVERT: A 275 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7668 (mm-30) REVERT: A 386 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8136 (mptt) REVERT: A 387 TRP cc_start: 0.7629 (m-90) cc_final: 0.7258 (m100) REVERT: A 570 GLU cc_start: 0.7979 (tt0) cc_final: 0.7726 (tt0) REVERT: A 630 ARG cc_start: 0.7514 (mtp-110) cc_final: 0.7304 (mtm-85) REVERT: A 674 ASP cc_start: 0.8375 (m-30) cc_final: 0.8033 (m-30) REVERT: A 687 ARG cc_start: 0.7344 (ttm110) cc_final: 0.7062 (ttp80) REVERT: A 800 ASP cc_start: 0.7751 (m-30) cc_final: 0.7546 (m-30) REVERT: A 903 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8000 (tt) REVERT: A 1059 SER cc_start: 0.8784 (m) cc_final: 0.8489 (p) REVERT: A 1083 GLU cc_start: 0.7314 (tp30) cc_final: 0.7049 (tm-30) outliers start: 11 outliers final: 1 residues processed: 131 average time/residue: 1.4881 time to fit residues: 204.7317 Evaluate side-chains 94 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain B residue 2 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 348 ASN A 758 GLN A1026 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7884 Z= 0.196 Angle : 0.555 7.662 10758 Z= 0.282 Chirality : 0.042 0.187 1270 Planarity : 0.006 0.049 1330 Dihedral : 13.801 165.812 1258 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.58 % Allowed : 8.12 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.80 (0.27), residues: 952 helix: 1.01 (0.26), residues: 368 sheet: 1.04 (0.43), residues: 147 loop : 0.05 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 379 HIS 0.003 0.000 HIS A1133 PHE 0.015 0.001 PHE A1135 TYR 0.009 0.001 TYR A 996 ARG 0.005 0.000 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.080 Fit side-chains REVERT: A 275 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7632 (mm-30) REVERT: A 327 SER cc_start: 0.8896 (OUTLIER) cc_final: 0.8685 (t) REVERT: A 348 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8173 (p0) REVERT: A 386 LYS cc_start: 0.8302 (ttmt) cc_final: 0.8060 (mptt) REVERT: A 674 ASP cc_start: 0.8331 (m-30) cc_final: 0.8000 (m-30) REVERT: A 723 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7336 (ttm110) REVERT: A 1059 SER cc_start: 0.8699 (m) cc_final: 0.8478 (p) REVERT: A 1083 GLU cc_start: 0.7445 (tp30) cc_final: 0.7131 (tm-30) outliers start: 13 outliers final: 6 residues processed: 107 average time/residue: 1.4779 time to fit residues: 166.3357 Evaluate side-chains 95 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain B residue 2 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 71 optimal weight: 0.1980 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 0.0170 chunk 93 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7884 Z= 0.150 Angle : 0.503 8.078 10758 Z= 0.255 Chirality : 0.041 0.161 1270 Planarity : 0.005 0.047 1330 Dihedral : 12.565 173.902 1258 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.21 % Allowed : 10.91 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.94 (0.27), residues: 952 helix: 1.11 (0.27), residues: 361 sheet: 1.12 (0.43), residues: 147 loop : 0.16 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 448 HIS 0.003 0.000 HIS A1133 PHE 0.007 0.001 PHE A1135 TYR 0.008 0.001 TYR A 743 ARG 0.002 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.928 Fit side-chains REVERT: A 275 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7715 (mm-30) REVERT: A 386 LYS cc_start: 0.8299 (ttmt) cc_final: 0.8061 (mptt) REVERT: A 674 ASP cc_start: 0.8326 (m-30) cc_final: 0.7999 (m-30) REVERT: A 723 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7398 (ttm110) REVERT: A 1083 GLU cc_start: 0.7480 (tp30) cc_final: 0.7109 (tm-30) outliers start: 10 outliers final: 7 residues processed: 98 average time/residue: 1.5463 time to fit residues: 159.4772 Evaluate side-chains 95 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 899 GLN Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 942 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 24 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: A 898 HIS A 907 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7884 Z= 0.238 Angle : 0.516 6.699 10758 Z= 0.262 Chirality : 0.041 0.136 1270 Planarity : 0.005 0.045 1330 Dihedral : 12.038 175.779 1257 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.45 % Allowed : 11.52 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.94 (0.27), residues: 952 helix: 0.97 (0.27), residues: 369 sheet: 0.94 (0.41), residues: 162 loop : 0.34 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 448 HIS 0.002 0.001 HIS A1133 PHE 0.011 0.001 PHE A1135 TYR 0.010 0.001 TYR A 996 ARG 0.002 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.785 Fit side-chains REVERT: A 275 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7820 (mm-30) REVERT: A 386 LYS cc_start: 0.8295 (ttmt) cc_final: 0.8072 (mptt) REVERT: A 572 MET cc_start: 0.8618 (ptp) cc_final: 0.8190 (mtm) REVERT: A 674 ASP cc_start: 0.8338 (m-30) cc_final: 0.7987 (m-30) REVERT: A 723 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7442 (ttm110) REVERT: A 1083 GLU cc_start: 0.7580 (tp30) cc_final: 0.7214 (tm-30) outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 1.6491 time to fit residues: 167.5880 Evaluate side-chains 98 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1021 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 63 optimal weight: 0.0030 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS A 907 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7884 Z= 0.160 Angle : 0.480 5.939 10758 Z= 0.245 Chirality : 0.040 0.131 1270 Planarity : 0.005 0.045 1330 Dihedral : 11.571 170.553 1257 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.21 % Allowed : 12.73 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.99 (0.27), residues: 952 helix: 1.03 (0.27), residues: 369 sheet: 0.88 (0.41), residues: 162 loop : 0.39 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 448 HIS 0.002 0.000 HIS A1133 PHE 0.007 0.001 PHE A 820 TYR 0.007 0.001 TYR A 996 ARG 0.002 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.894 Fit side-chains REVERT: A 275 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7780 (mm-30) REVERT: A 386 LYS cc_start: 0.8265 (ttmt) cc_final: 0.8017 (mptt) REVERT: A 572 MET cc_start: 0.8586 (ptp) cc_final: 0.8097 (mtm) REVERT: A 674 ASP cc_start: 0.8292 (m-30) cc_final: 0.7941 (m-30) REVERT: A 687 ARG cc_start: 0.7441 (ttm110) cc_final: 0.6998 (ttt180) REVERT: A 723 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7451 (ttm110) REVERT: A 1073 PHE cc_start: 0.7562 (m-10) cc_final: 0.6220 (t80) REVERT: A 1083 GLU cc_start: 0.7569 (tp30) cc_final: 0.7215 (tm-30) outliers start: 10 outliers final: 8 residues processed: 94 average time/residue: 1.7943 time to fit residues: 176.8130 Evaluate side-chains 97 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 942 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 0.0370 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 48 optimal weight: 0.0050 chunk 88 optimal weight: 2.9990 overall best weight: 0.5272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS A 907 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7884 Z= 0.147 Angle : 0.476 6.339 10758 Z= 0.241 Chirality : 0.040 0.130 1270 Planarity : 0.005 0.044 1330 Dihedral : 11.105 163.714 1257 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.97 % Allowed : 13.58 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.28), residues: 952 helix: 1.11 (0.27), residues: 369 sheet: 0.75 (0.39), residues: 176 loop : 0.55 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 448 HIS 0.003 0.000 HIS A1133 PHE 0.006 0.001 PHE A 820 TYR 0.007 0.001 TYR A 743 ARG 0.002 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.959 Fit side-chains REVERT: A 275 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7814 (mm-30) REVERT: A 386 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7964 (mptt) REVERT: A 572 MET cc_start: 0.8602 (ptp) cc_final: 0.8085 (mtm) REVERT: A 575 SER cc_start: 0.7689 (OUTLIER) cc_final: 0.7278 (m) REVERT: A 674 ASP cc_start: 0.8276 (m-30) cc_final: 0.7924 (m-30) REVERT: A 687 ARG cc_start: 0.7426 (ttm110) cc_final: 0.7023 (ttt180) REVERT: A 723 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7444 (ttm110) REVERT: A 1073 PHE cc_start: 0.7544 (m-10) cc_final: 0.6232 (t80) REVERT: A 1083 GLU cc_start: 0.7584 (tp30) cc_final: 0.7281 (tm-30) outliers start: 8 outliers final: 5 residues processed: 101 average time/residue: 1.5496 time to fit residues: 164.4641 Evaluate side-chains 98 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1021 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 0.0970 chunk 77 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 GLN A 898 HIS A 907 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7884 Z= 0.166 Angle : 0.491 8.476 10758 Z= 0.246 Chirality : 0.040 0.130 1270 Planarity : 0.005 0.043 1330 Dihedral : 10.928 159.869 1257 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.33 % Allowed : 13.70 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.28), residues: 952 helix: 1.11 (0.27), residues: 369 sheet: 0.77 (0.39), residues: 176 loop : 0.60 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 448 HIS 0.002 0.000 HIS A1133 PHE 0.007 0.001 PHE A 911 TYR 0.008 0.001 TYR A 996 ARG 0.001 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.951 Fit side-chains REVERT: A 275 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7891 (mm-30) REVERT: A 386 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7987 (mptt) REVERT: A 527 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6429 (pm20) REVERT: A 572 MET cc_start: 0.8621 (ptp) cc_final: 0.8111 (mtm) REVERT: A 575 SER cc_start: 0.7697 (OUTLIER) cc_final: 0.7283 (m) REVERT: A 674 ASP cc_start: 0.8275 (m-30) cc_final: 0.7926 (m-30) REVERT: A 687 ARG cc_start: 0.7442 (ttm110) cc_final: 0.7028 (ttt180) REVERT: A 723 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7461 (ttm110) REVERT: A 1073 PHE cc_start: 0.7539 (m-10) cc_final: 0.6239 (t80) REVERT: A 1083 GLU cc_start: 0.7599 (tp30) cc_final: 0.7299 (tm-30) outliers start: 11 outliers final: 7 residues processed: 97 average time/residue: 1.5572 time to fit residues: 158.8199 Evaluate side-chains 102 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1021 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 17 optimal weight: 0.0030 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 83 optimal weight: 0.0980 chunk 87 optimal weight: 8.9990 chunk 80 optimal weight: 0.0040 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS A 899 GLN A 907 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7884 Z= 0.144 Angle : 0.484 9.051 10758 Z= 0.242 Chirality : 0.040 0.136 1270 Planarity : 0.004 0.043 1330 Dihedral : 10.622 155.204 1257 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.58 % Allowed : 13.21 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 952 helix: 1.17 (0.27), residues: 369 sheet: 0.64 (0.38), residues: 179 loop : 0.61 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 448 HIS 0.002 0.000 HIS A1133 PHE 0.006 0.001 PHE A 627 TYR 0.007 0.001 TYR A 743 ARG 0.002 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.927 Fit side-chains REVERT: A 275 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7841 (mm-30) REVERT: A 386 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7983 (mptt) REVERT: A 527 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6438 (pm20) REVERT: A 572 MET cc_start: 0.8616 (ptp) cc_final: 0.8070 (mtm) REVERT: A 575 SER cc_start: 0.7708 (OUTLIER) cc_final: 0.7311 (m) REVERT: A 674 ASP cc_start: 0.8262 (m-30) cc_final: 0.7911 (m-30) REVERT: A 687 ARG cc_start: 0.7429 (ttm110) cc_final: 0.7028 (ttt180) REVERT: A 723 ARG cc_start: 0.8013 (mtp85) cc_final: 0.7472 (ttm110) REVERT: A 1073 PHE cc_start: 0.7571 (m-10) cc_final: 0.6275 (t80) REVERT: A 1083 GLU cc_start: 0.7612 (tp30) cc_final: 0.7322 (tm-30) outliers start: 13 outliers final: 8 residues processed: 103 average time/residue: 1.5144 time to fit residues: 164.2637 Evaluate side-chains 104 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 942 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 80 optimal weight: 0.1980 chunk 56 optimal weight: 0.0010 chunk 90 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS A 907 GLN A1057 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7884 Z= 0.156 Angle : 0.492 9.135 10758 Z= 0.245 Chirality : 0.040 0.141 1270 Planarity : 0.004 0.043 1330 Dihedral : 10.469 152.795 1257 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.58 % Allowed : 13.45 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.28), residues: 952 helix: 1.19 (0.27), residues: 368 sheet: 0.76 (0.38), residues: 177 loop : 0.68 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 448 HIS 0.002 0.000 HIS A1133 PHE 0.006 0.001 PHE A 911 TYR 0.007 0.001 TYR A 743 ARG 0.002 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.855 Fit side-chains REVERT: A 275 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7821 (mm-30) REVERT: A 386 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7987 (mptt) REVERT: A 505 THR cc_start: 0.7910 (m) cc_final: 0.7633 (m) REVERT: A 572 MET cc_start: 0.8620 (ptp) cc_final: 0.8135 (mtm) REVERT: A 575 SER cc_start: 0.7718 (OUTLIER) cc_final: 0.7322 (m) REVERT: A 674 ASP cc_start: 0.8253 (m-30) cc_final: 0.7905 (m-30) REVERT: A 723 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7484 (ttm110) REVERT: A 1073 PHE cc_start: 0.7570 (m-10) cc_final: 0.6274 (t80) REVERT: A 1083 GLU cc_start: 0.7623 (tp30) cc_final: 0.7327 (tm-30) outliers start: 13 outliers final: 9 residues processed: 103 average time/residue: 1.5449 time to fit residues: 167.2805 Evaluate side-chains 104 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1021 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 GLN A 898 HIS A 907 GLN A1057 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7884 Z= 0.152 Angle : 0.491 9.237 10758 Z= 0.245 Chirality : 0.040 0.155 1270 Planarity : 0.005 0.043 1330 Dihedral : 10.253 149.960 1257 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.09 % Allowed : 14.06 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.28), residues: 952 helix: 1.20 (0.27), residues: 368 sheet: 0.78 (0.38), residues: 177 loop : 0.72 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 448 HIS 0.002 0.000 HIS A1133 PHE 0.006 0.001 PHE A 911 TYR 0.007 0.001 TYR A 743 ARG 0.005 0.000 ARG A1022 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.811 Fit side-chains REVERT: A 275 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7828 (mm-30) REVERT: A 386 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7985 (mptt) REVERT: A 505 THR cc_start: 0.7917 (m) cc_final: 0.7639 (m) REVERT: A 572 MET cc_start: 0.8621 (ptp) cc_final: 0.8141 (mtm) REVERT: A 575 SER cc_start: 0.7723 (OUTLIER) cc_final: 0.7330 (m) REVERT: A 674 ASP cc_start: 0.8249 (m-30) cc_final: 0.7901 (m-30) REVERT: A 723 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7475 (ttm110) REVERT: A 1073 PHE cc_start: 0.7553 (m-10) cc_final: 0.6276 (t80) REVERT: A 1083 GLU cc_start: 0.7624 (tp30) cc_final: 0.7328 (tm-30) outliers start: 9 outliers final: 7 residues processed: 101 average time/residue: 1.4850 time to fit residues: 157.4314 Evaluate side-chains 102 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 942 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 0.0770 chunk 75 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN A 898 HIS A 907 GLN A1057 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102440 restraints weight = 9622.786| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.99 r_work: 0.3177 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7884 Z= 0.135 Angle : 0.484 9.487 10758 Z= 0.240 Chirality : 0.040 0.182 1270 Planarity : 0.004 0.043 1330 Dihedral : 9.787 146.455 1255 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.97 % Allowed : 14.18 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.28), residues: 952 helix: 1.26 (0.28), residues: 368 sheet: 0.71 (0.38), residues: 179 loop : 0.77 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 448 HIS 0.002 0.000 HIS A1133 PHE 0.005 0.001 PHE A 911 TYR 0.007 0.001 TYR A 743 ARG 0.004 0.000 ARG A1022 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3481.92 seconds wall clock time: 62 minutes 56.93 seconds (3776.93 seconds total)