Starting phenix.real_space_refine on Wed Apr 30 11:42:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lbs_62955/04_2025/9lbs_62955.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lbs_62955/04_2025/9lbs_62955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lbs_62955/04_2025/9lbs_62955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lbs_62955/04_2025/9lbs_62955.map" model { file = "/net/cci-nas-00/data/ceres_data/9lbs_62955/04_2025/9lbs_62955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lbs_62955/04_2025/9lbs_62955.cif" } resolution = 3.41 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3508 atoms to isotropic. 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 26 5.16 5 C 4254 2.51 5 N 1130 2.21 5 O 1320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6730 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 976 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "B" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "D" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 894 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "F" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1462 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 171} Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 819 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.48, per 1000 atoms: 0.81 Number of scatterers: 6730 At special positions: 0 Unit cell: (71.69, 113.9, 120.6, 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 26 16.00 O 1320 8.00 N 1130 7.00 C 4254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.01 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG E 1 " - " ASN F 343 " Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 1.0 seconds 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1552 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 20 sheets defined 3.8% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.737A pdb=" N ASP A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.535A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 76 removed outlier: 3.555A pdb=" N LYS D 75 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 405 through 411 removed outlier: 5.034A pdb=" N SER F 408 " --> pdb=" O ASN F 405 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA F 411 " --> pdb=" O SER F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.605A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 80 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 71 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR A 69 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.959A pdb=" N ALA A 92 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 40 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.309A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLN B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU B 47 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA6, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.693A pdb=" N SER B 66 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.604A pdb=" N GLN B 91 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B 97 " --> pdb=" O GLN B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.583A pdb=" N TYR H 58 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR H 93 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR H 114 " --> pdb=" O TYR H 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 70 through 72 removed outlier: 3.880A pdb=" N SER H 77 " --> pdb=" O GLU H 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 97 through 100 removed outlier: 4.145A pdb=" N ARG H 97 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.159A pdb=" N LYS L 104 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 20 through 22 removed outlier: 4.092A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU L 73 " --> pdb=" O ILE L 21 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 18 through 19 removed outlier: 3.548A pdb=" N MET D 82 " --> pdb=" O LEU D 18 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 57 through 58 removed outlier: 3.661A pdb=" N TYR D 58 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 50 " --> pdb=" O TYR D 58 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR D 33 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 98 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE D 107 " --> pdb=" O ARG D 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 57 through 58 removed outlier: 3.661A pdb=" N TYR D 58 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 50 " --> pdb=" O TYR D 58 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR D 33 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 98 " --> pdb=" O TYR D 33 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 400 through 403 Processing sheet with id=AB8, first strand: chain 'F' and resid 452 through 453 Processing sheet with id=AB9, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AC1, first strand: chain 'C' and resid 18 through 22 removed outlier: 3.672A pdb=" N ALA C 70 " --> pdb=" O CYS C 22 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR C 69 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 44 through 47 removed outlier: 6.106A pdb=" N LEU C 45 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLN C 36 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 47 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 98 " --> pdb=" O VAL C 89 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 270 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: 1.82 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2139 1.35 - 1.47: 1941 1.47 - 1.60: 2787 1.60 - 1.72: 0 1.72 - 1.84: 34 Bond restraints: 6901 Sorted by residual: bond pdb=" C PHE F 456 " pdb=" N ARG F 457 " ideal model delta sigma weight residual 1.331 1.410 -0.079 1.23e-02 6.61e+03 4.11e+01 bond pdb=" C SER D 49 " pdb=" N VAL D 50 " ideal model delta sigma weight residual 1.330 1.376 -0.046 1.21e-02 6.83e+03 1.42e+01 bond pdb=" N TYR A 27 " pdb=" CA TYR A 27 " ideal model delta sigma weight residual 1.455 1.486 -0.032 9.60e-03 1.09e+04 1.08e+01 bond pdb=" N VAL H 118 " pdb=" CA VAL H 118 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" N VAL H 48 " pdb=" CA VAL H 48 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.20e-02 6.94e+03 8.36e+00 ... (remaining 6896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 9058 1.88 - 3.77: 276 3.77 - 5.65: 30 5.65 - 7.53: 13 7.53 - 9.42: 4 Bond angle restraints: 9381 Sorted by residual: angle pdb=" N PRO D 101 " pdb=" CA PRO D 101 " pdb=" C PRO D 101 " ideal model delta sigma weight residual 110.70 117.40 -6.70 1.22e+00 6.72e-01 3.02e+01 angle pdb=" C LYS F 458 " pdb=" N SER F 459 " pdb=" CA SER F 459 " ideal model delta sigma weight residual 121.54 130.00 -8.46 1.91e+00 2.74e-01 1.96e+01 angle pdb=" CA PHE F 456 " pdb=" CB PHE F 456 " pdb=" CG PHE F 456 " ideal model delta sigma weight residual 113.80 117.89 -4.09 1.00e+00 1.00e+00 1.67e+01 angle pdb=" CA GLU B 82 " pdb=" CB GLU B 82 " pdb=" CG GLU B 82 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CA LYS F 458 " pdb=" CB LYS F 458 " pdb=" CG LYS F 458 " ideal model delta sigma weight residual 114.10 121.51 -7.41 2.00e+00 2.50e-01 1.37e+01 ... (remaining 9376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 3469 17.54 - 35.08: 439 35.08 - 52.62: 102 52.62 - 70.16: 30 70.16 - 87.70: 14 Dihedral angle restraints: 4054 sinusoidal: 1583 harmonic: 2471 Sorted by residual: dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 89 " pdb=" CB CYS B 89 " ideal model delta sinusoidal sigma weight residual 93.00 -179.30 -87.70 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 95 " pdb=" CB CYS D 95 " ideal model delta sinusoidal sigma weight residual 93.00 148.59 -55.59 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 4051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 981 0.118 - 0.236: 26 0.236 - 0.354: 2 0.354 - 0.472: 0 0.472 - 0.589: 1 Chirality restraints: 1010 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.37e+02 chirality pdb=" C1 FUC E 3 " pdb=" O6 NAG E 1 " pdb=" C2 FUC E 3 " pdb=" O5 FUC E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.53e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN F 343 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.69e+00 ... (remaining 1007 not shown) Planarity restraints: 1208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.064 2.00e-02 2.50e+03 5.30e-02 3.51e+01 pdb=" C7 NAG E 1 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.049 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.084 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 50 " 0.023 2.00e-02 2.50e+03 2.98e-02 2.22e+01 pdb=" CG TRP A 50 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP A 50 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP A 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 50 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 50 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 50 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 50 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 55 " -0.220 9.50e-02 1.11e+02 9.85e-02 5.95e+00 pdb=" NE ARG B 55 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 55 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 55 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 55 " -0.008 2.00e-02 2.50e+03 ... (remaining 1205 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 819 2.75 - 3.29: 6171 3.29 - 3.83: 10576 3.83 - 4.36: 12019 4.36 - 4.90: 21069 Nonbonded interactions: 50654 Sorted by model distance: nonbonded pdb=" O SER H 101 " pdb=" OG SER H 101 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR D 52 " pdb=" OD2 ASP C 95 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR F 369 " pdb=" O PRO F 384 " model vdw 2.274 3.040 nonbonded pdb=" O TYR C 85 " pdb=" OG1 THR C 103 " model vdw 2.295 3.040 ... (remaining 50649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 20.210 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6912 Z= 0.271 Angle : 0.769 9.418 9406 Z= 0.427 Chirality : 0.052 0.589 1010 Planarity : 0.006 0.098 1207 Dihedral : 17.047 87.546 2478 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.08 % Favored : 87.46 % Rotamer: Outliers : 0.69 % Allowed : 27.29 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.57 (0.27), residues: 853 helix: -4.26 (0.80), residues: 21 sheet: -1.68 (0.34), residues: 265 loop : -2.81 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.003 TRP A 50 HIS 0.006 0.001 HIS H 35 PHE 0.031 0.002 PHE D 67 TYR 0.021 0.001 TYR F 473 ARG 0.002 0.000 ARG F 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 1) link_NAG-ASN : angle 2.71442 ( 3) link_BETA1-4 : bond 0.04762 ( 1) link_BETA1-4 : angle 4.99030 ( 3) hydrogen bonds : bond 0.32914 ( 112) hydrogen bonds : angle 10.41253 ( 270) link_BETA1-6 : bond 0.03555 ( 1) link_BETA1-6 : angle 4.43315 ( 3) SS BOND : bond 0.00791 ( 8) SS BOND : angle 1.60420 ( 16) covalent geometry : bond 0.00435 ( 6901) covalent geometry : angle 0.75650 ( 9381) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 6 GLN cc_start: 0.6296 (pt0) cc_final: 0.6082 (pt0) REVERT: L 99 PHE cc_start: 0.8010 (m-10) cc_final: 0.7678 (m-10) outliers start: 5 outliers final: 3 residues processed: 124 average time/residue: 0.1998 time to fit residues: 32.9039 Evaluate side-chains 122 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain C residue 66 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 6 GLN L 79 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.151704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132658 restraints weight = 10208.598| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.12 r_work: 0.3650 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6912 Z= 0.197 Angle : 0.684 9.075 9406 Z= 0.356 Chirality : 0.044 0.157 1010 Planarity : 0.005 0.057 1207 Dihedral : 5.326 35.866 1025 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.25 % Favored : 86.64 % Rotamer: Outliers : 5.26 % Allowed : 22.16 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.37 (0.28), residues: 853 helix: -4.15 (0.80), residues: 21 sheet: -1.33 (0.34), residues: 280 loop : -2.82 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 50 HIS 0.008 0.002 HIS H 35 PHE 0.019 0.002 PHE D 67 TYR 0.017 0.002 TYR L 32 ARG 0.004 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00644 ( 1) link_NAG-ASN : angle 0.60188 ( 3) link_BETA1-4 : bond 0.00555 ( 1) link_BETA1-4 : angle 1.35204 ( 3) hydrogen bonds : bond 0.05426 ( 112) hydrogen bonds : angle 7.78717 ( 270) link_BETA1-6 : bond 0.00657 ( 1) link_BETA1-6 : angle 1.32893 ( 3) SS BOND : bond 0.00416 ( 8) SS BOND : angle 0.94017 ( 16) covalent geometry : bond 0.00441 ( 6901) covalent geometry : angle 0.68276 ( 9381) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 TRP cc_start: 0.8159 (t60) cc_final: 0.7837 (t60) REVERT: B 38 GLN cc_start: 0.8059 (tt0) cc_final: 0.7594 (tt0) REVERT: H 80 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7438 (tt) REVERT: H 97 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6727 (mmm-85) REVERT: L 6 GLN cc_start: 0.6893 (pt0) cc_final: 0.6625 (pt0) REVERT: D 13 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8424 (mm-40) REVERT: C 74 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7259 (mt) outliers start: 38 outliers final: 22 residues processed: 151 average time/residue: 0.1797 time to fit residues: 37.5870 Evaluate side-chains 148 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 74 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN B 6 GLN D 32 ASN F 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.151927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133271 restraints weight = 10203.112| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.07 r_work: 0.3653 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6912 Z= 0.178 Angle : 0.668 8.978 9406 Z= 0.346 Chirality : 0.044 0.185 1010 Planarity : 0.005 0.057 1207 Dihedral : 5.344 38.914 1024 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.54 % Favored : 87.34 % Rotamer: Outliers : 4.85 % Allowed : 23.68 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.33 (0.27), residues: 853 helix: -3.96 (0.88), residues: 21 sheet: -1.26 (0.33), residues: 279 loop : -2.82 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 47 HIS 0.006 0.002 HIS H 35 PHE 0.013 0.001 PHE D 67 TYR 0.013 0.001 TYR L 32 ARG 0.002 0.000 ARG B 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 1) link_NAG-ASN : angle 0.64958 ( 3) link_BETA1-4 : bond 0.00458 ( 1) link_BETA1-4 : angle 1.19805 ( 3) hydrogen bonds : bond 0.04752 ( 112) hydrogen bonds : angle 7.35346 ( 270) link_BETA1-6 : bond 0.00439 ( 1) link_BETA1-6 : angle 1.30158 ( 3) SS BOND : bond 0.00525 ( 8) SS BOND : angle 1.46139 ( 16) covalent geometry : bond 0.00404 ( 6901) covalent geometry : angle 0.66568 ( 9381) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.6693 (tpt) cc_final: 0.6313 (tpt) REVERT: A 50 TRP cc_start: 0.8136 (t60) cc_final: 0.7788 (t60) REVERT: B 38 GLN cc_start: 0.8074 (tt0) cc_final: 0.7582 (tt0) REVERT: H 78 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7376 (tp) REVERT: H 80 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7448 (tt) REVERT: H 97 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6734 (mmm-85) REVERT: L 6 GLN cc_start: 0.6914 (pt0) cc_final: 0.6641 (pt0) REVERT: L 99 PHE cc_start: 0.8227 (m-80) cc_final: 0.7817 (m-10) REVERT: D 13 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8474 (mm-40) REVERT: C 5 THR cc_start: 0.7300 (OUTLIER) cc_final: 0.6947 (p) REVERT: C 74 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7217 (mt) outliers start: 35 outliers final: 21 residues processed: 152 average time/residue: 0.1880 time to fit residues: 38.7679 Evaluate side-chains 152 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 473 TYR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 74 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 80 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 77 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.152424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.133672 restraints weight = 10309.385| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.01 r_work: 0.3672 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6912 Z= 0.140 Angle : 0.633 9.101 9406 Z= 0.329 Chirality : 0.043 0.158 1010 Planarity : 0.005 0.056 1207 Dihedral : 5.255 41.831 1024 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.84 % Favored : 88.04 % Rotamer: Outliers : 5.96 % Allowed : 23.68 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.26 (0.27), residues: 853 helix: -3.84 (0.94), residues: 20 sheet: -1.25 (0.32), residues: 287 loop : -2.78 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.001 PHE D 67 TYR 0.011 0.001 TYR F 473 ARG 0.002 0.000 ARG F 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 1) link_NAG-ASN : angle 0.60467 ( 3) link_BETA1-4 : bond 0.00488 ( 1) link_BETA1-4 : angle 1.04976 ( 3) hydrogen bonds : bond 0.04017 ( 112) hydrogen bonds : angle 7.02289 ( 270) link_BETA1-6 : bond 0.00408 ( 1) link_BETA1-6 : angle 1.27492 ( 3) SS BOND : bond 0.00420 ( 8) SS BOND : angle 0.98527 ( 16) covalent geometry : bond 0.00321 ( 6901) covalent geometry : angle 0.63151 ( 9381) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.7849 (m-80) cc_final: 0.7640 (m-10) REVERT: A 50 TRP cc_start: 0.8056 (t60) cc_final: 0.7783 (t60) REVERT: A 96 CYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7289 (p) REVERT: B 38 GLN cc_start: 0.7996 (tt0) cc_final: 0.7689 (tt0) REVERT: B 55 ARG cc_start: 0.8340 (mtp-110) cc_final: 0.8068 (mtp85) REVERT: H 78 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7441 (tp) REVERT: H 80 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7380 (tt) REVERT: H 97 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6767 (mmm-85) REVERT: L 88 CYS cc_start: 0.4435 (OUTLIER) cc_final: 0.4152 (m) REVERT: L 99 PHE cc_start: 0.8176 (m-80) cc_final: 0.7778 (m-10) REVERT: D 13 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8480 (mm-40) REVERT: C 5 THR cc_start: 0.7271 (OUTLIER) cc_final: 0.6942 (p) REVERT: C 74 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7202 (mt) outliers start: 43 outliers final: 27 residues processed: 163 average time/residue: 0.1794 time to fit residues: 39.1541 Evaluate side-chains 159 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 CYS Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 473 TYR Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 89 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 47 optimal weight: 0.0970 chunk 80 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 81 optimal weight: 0.0770 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 6 GLN L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.152820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.134039 restraints weight = 10153.416| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.99 r_work: 0.3675 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6912 Z= 0.143 Angle : 0.644 8.984 9406 Z= 0.330 Chirality : 0.043 0.183 1010 Planarity : 0.005 0.057 1207 Dihedral : 5.259 44.071 1024 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.72 % Favored : 88.16 % Rotamer: Outliers : 5.96 % Allowed : 23.82 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.29 (0.27), residues: 853 helix: -3.86 (0.90), residues: 20 sheet: -1.30 (0.32), residues: 290 loop : -2.78 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 36 HIS 0.006 0.002 HIS H 35 PHE 0.010 0.001 PHE C 61 TYR 0.012 0.001 TYR D 79 ARG 0.002 0.000 ARG B 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 1) link_NAG-ASN : angle 0.61680 ( 3) link_BETA1-4 : bond 0.00355 ( 1) link_BETA1-4 : angle 1.10502 ( 3) hydrogen bonds : bond 0.03915 ( 112) hydrogen bonds : angle 6.85095 ( 270) link_BETA1-6 : bond 0.00426 ( 1) link_BETA1-6 : angle 1.25310 ( 3) SS BOND : bond 0.00381 ( 8) SS BOND : angle 1.02459 ( 16) covalent geometry : bond 0.00324 ( 6901) covalent geometry : angle 0.64236 ( 9381) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TRP cc_start: 0.8049 (t60) cc_final: 0.7793 (t60) REVERT: B 38 GLN cc_start: 0.8004 (tt0) cc_final: 0.7710 (tt0) REVERT: B 55 ARG cc_start: 0.8350 (mtp-110) cc_final: 0.8094 (mtp85) REVERT: H 78 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7521 (tp) REVERT: H 80 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7487 (tt) REVERT: H 97 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6767 (mmm-85) REVERT: L 99 PHE cc_start: 0.8157 (m-80) cc_final: 0.7738 (m-10) REVERT: C 5 THR cc_start: 0.7293 (OUTLIER) cc_final: 0.6973 (p) REVERT: C 74 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7164 (mt) outliers start: 43 outliers final: 31 residues processed: 157 average time/residue: 0.1931 time to fit residues: 40.9334 Evaluate side-chains 159 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 473 TYR Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 43 optimal weight: 0.0870 chunk 1 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 6 GLN L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.154460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.135627 restraints weight = 10116.986| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.07 r_work: 0.3689 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6912 Z= 0.112 Angle : 0.627 8.887 9406 Z= 0.322 Chirality : 0.043 0.172 1010 Planarity : 0.004 0.057 1207 Dihedral : 5.136 44.983 1024 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.37 % Favored : 88.51 % Rotamer: Outliers : 5.12 % Allowed : 25.35 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.23 (0.27), residues: 853 helix: -3.87 (0.92), residues: 20 sheet: -1.22 (0.32), residues: 289 loop : -2.76 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 36 HIS 0.005 0.001 HIS H 35 PHE 0.009 0.001 PHE D 67 TYR 0.016 0.001 TYR D 79 ARG 0.002 0.000 ARG F 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 1) link_NAG-ASN : angle 0.55909 ( 3) link_BETA1-4 : bond 0.00355 ( 1) link_BETA1-4 : angle 1.02802 ( 3) hydrogen bonds : bond 0.03464 ( 112) hydrogen bonds : angle 6.68525 ( 270) link_BETA1-6 : bond 0.00458 ( 1) link_BETA1-6 : angle 1.31164 ( 3) SS BOND : bond 0.00473 ( 8) SS BOND : angle 1.04270 ( 16) covalent geometry : bond 0.00253 ( 6901) covalent geometry : angle 0.62526 ( 9381) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TRP cc_start: 0.7990 (t60) cc_final: 0.7789 (t60) REVERT: A 96 CYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7303 (p) REVERT: B 38 GLN cc_start: 0.8020 (tt0) cc_final: 0.7575 (tt0) REVERT: B 55 ARG cc_start: 0.8328 (mtp-110) cc_final: 0.8090 (mtp85) REVERT: H 78 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7600 (tp) REVERT: H 97 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6694 (mmm-85) REVERT: L 99 PHE cc_start: 0.8132 (m-80) cc_final: 0.7727 (m-10) REVERT: C 5 THR cc_start: 0.7267 (OUTLIER) cc_final: 0.6946 (p) REVERT: C 74 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7106 (mt) outliers start: 37 outliers final: 27 residues processed: 147 average time/residue: 0.1660 time to fit residues: 33.1093 Evaluate side-chains 152 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 74 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 72 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 17 optimal weight: 0.0470 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.152229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.133404 restraints weight = 10192.061| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.98 r_work: 0.3664 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6912 Z= 0.171 Angle : 0.654 8.781 9406 Z= 0.336 Chirality : 0.044 0.199 1010 Planarity : 0.005 0.056 1207 Dihedral : 5.272 47.048 1024 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.31 % Favored : 87.57 % Rotamer: Outliers : 5.12 % Allowed : 25.48 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.24 (0.27), residues: 853 helix: -3.88 (1.16), residues: 14 sheet: -1.29 (0.31), residues: 294 loop : -2.76 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 36 HIS 0.006 0.002 HIS H 35 PHE 0.013 0.001 PHE C 61 TYR 0.015 0.001 TYR D 79 ARG 0.002 0.000 ARG A 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 1) link_NAG-ASN : angle 0.71183 ( 3) link_BETA1-4 : bond 0.00400 ( 1) link_BETA1-4 : angle 1.19887 ( 3) hydrogen bonds : bond 0.03976 ( 112) hydrogen bonds : angle 6.71596 ( 270) link_BETA1-6 : bond 0.00632 ( 1) link_BETA1-6 : angle 1.28487 ( 3) SS BOND : bond 0.00445 ( 8) SS BOND : angle 1.14576 ( 16) covalent geometry : bond 0.00389 ( 6901) covalent geometry : angle 0.65212 ( 9381) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.7862 (m-80) cc_final: 0.7546 (m-10) REVERT: A 48 MET cc_start: 0.6787 (tpt) cc_final: 0.6345 (tpt) REVERT: A 50 TRP cc_start: 0.8048 (t60) cc_final: 0.7772 (t60) REVERT: B 38 GLN cc_start: 0.8042 (tt0) cc_final: 0.7634 (tt0) REVERT: B 55 ARG cc_start: 0.8338 (mtp-110) cc_final: 0.8100 (mtp85) REVERT: H 78 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7613 (tp) REVERT: H 97 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6829 (mmm-85) REVERT: L 6 GLN cc_start: 0.6810 (pt0) cc_final: 0.6555 (pt0) REVERT: L 99 PHE cc_start: 0.8149 (m-80) cc_final: 0.7749 (m-10) REVERT: C 5 THR cc_start: 0.7286 (OUTLIER) cc_final: 0.6978 (p) REVERT: C 74 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7130 (mt) outliers start: 37 outliers final: 28 residues processed: 148 average time/residue: 0.1896 time to fit residues: 37.5853 Evaluate side-chains 152 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 74 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 44 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 0.0470 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.152898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.134157 restraints weight = 10232.935| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.98 r_work: 0.3673 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6912 Z= 0.136 Angle : 0.637 8.819 9406 Z= 0.326 Chirality : 0.043 0.195 1010 Planarity : 0.004 0.055 1207 Dihedral : 5.247 48.765 1024 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.25 % Favored : 88.63 % Rotamer: Outliers : 5.12 % Allowed : 25.21 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.19 (0.27), residues: 853 helix: -3.85 (1.19), residues: 14 sheet: -1.21 (0.32), residues: 290 loop : -2.74 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 36 HIS 0.006 0.002 HIS H 35 PHE 0.009 0.001 PHE C 61 TYR 0.014 0.001 TYR D 79 ARG 0.004 0.000 ARG A 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 1) link_NAG-ASN : angle 0.70160 ( 3) link_BETA1-4 : bond 0.00249 ( 1) link_BETA1-4 : angle 1.08964 ( 3) hydrogen bonds : bond 0.03596 ( 112) hydrogen bonds : angle 6.64393 ( 270) link_BETA1-6 : bond 0.00362 ( 1) link_BETA1-6 : angle 1.24697 ( 3) SS BOND : bond 0.00399 ( 8) SS BOND : angle 0.98810 ( 16) covalent geometry : bond 0.00309 ( 6901) covalent geometry : angle 0.63552 ( 9381) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.7826 (m-80) cc_final: 0.7451 (m-10) REVERT: A 38 ARG cc_start: 0.8041 (ttp-170) cc_final: 0.7678 (ttp80) REVERT: A 50 TRP cc_start: 0.8001 (t60) cc_final: 0.7727 (t60) REVERT: B 38 GLN cc_start: 0.8011 (tt0) cc_final: 0.7602 (tt0) REVERT: B 55 ARG cc_start: 0.8336 (mtp-110) cc_final: 0.8110 (mtp85) REVERT: H 78 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7587 (tp) REVERT: H 97 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6787 (mmm-85) REVERT: L 6 GLN cc_start: 0.6808 (pt0) cc_final: 0.6556 (pt0) REVERT: L 99 PHE cc_start: 0.8147 (m-80) cc_final: 0.7730 (m-10) REVERT: C 5 THR cc_start: 0.7275 (OUTLIER) cc_final: 0.6967 (p) REVERT: C 74 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7128 (mt) outliers start: 37 outliers final: 28 residues processed: 149 average time/residue: 0.1841 time to fit residues: 36.8084 Evaluate side-chains 153 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 74 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.151523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132734 restraints weight = 10279.322| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.97 r_work: 0.3661 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6912 Z= 0.174 Angle : 0.673 9.422 9406 Z= 0.346 Chirality : 0.044 0.224 1010 Planarity : 0.004 0.055 1207 Dihedral : 5.372 50.543 1024 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.78 % Favored : 87.10 % Rotamer: Outliers : 4.99 % Allowed : 25.07 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.23 (0.27), residues: 853 helix: -3.97 (1.08), residues: 14 sheet: -1.29 (0.31), residues: 296 loop : -2.74 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 36 HIS 0.008 0.002 HIS H 35 PHE 0.012 0.001 PHE C 61 TYR 0.014 0.001 TYR D 79 ARG 0.005 0.000 ARG A 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00637 ( 1) link_NAG-ASN : angle 0.81617 ( 3) link_BETA1-4 : bond 0.00422 ( 1) link_BETA1-4 : angle 1.15180 ( 3) hydrogen bonds : bond 0.03913 ( 112) hydrogen bonds : angle 6.67438 ( 270) link_BETA1-6 : bond 0.00529 ( 1) link_BETA1-6 : angle 1.26515 ( 3) SS BOND : bond 0.00727 ( 8) SS BOND : angle 1.29356 ( 16) covalent geometry : bond 0.00394 ( 6901) covalent geometry : angle 0.67129 ( 9381) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.7844 (m-80) cc_final: 0.7566 (m-10) REVERT: A 48 MET cc_start: 0.6798 (tpt) cc_final: 0.6461 (tpt) REVERT: A 50 TRP cc_start: 0.8019 (t60) cc_final: 0.7699 (t60) REVERT: B 38 GLN cc_start: 0.8041 (tt0) cc_final: 0.7641 (tt0) REVERT: B 55 ARG cc_start: 0.8343 (mtp-110) cc_final: 0.8110 (mtp85) REVERT: H 78 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7613 (tp) REVERT: H 97 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6831 (mmm-85) REVERT: L 6 GLN cc_start: 0.6840 (pt0) cc_final: 0.6564 (pt0) REVERT: L 99 PHE cc_start: 0.8150 (m-80) cc_final: 0.7720 (m-10) REVERT: C 5 THR cc_start: 0.7267 (OUTLIER) cc_final: 0.6976 (p) REVERT: C 74 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7149 (mt) outliers start: 36 outliers final: 27 residues processed: 147 average time/residue: 0.2069 time to fit residues: 40.9753 Evaluate side-chains 151 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 10 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 27 optimal weight: 0.0870 chunk 65 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.153740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.134736 restraints weight = 10316.961| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.10 r_work: 0.3680 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6912 Z= 0.122 Angle : 0.645 8.798 9406 Z= 0.328 Chirality : 0.044 0.206 1010 Planarity : 0.004 0.056 1207 Dihedral : 5.208 50.570 1024 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.02 % Favored : 88.86 % Rotamer: Outliers : 3.60 % Allowed : 26.45 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.14 (0.27), residues: 853 helix: -3.91 (1.15), residues: 14 sheet: -1.17 (0.31), residues: 292 loop : -2.71 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 47 HIS 0.006 0.001 HIS H 35 PHE 0.012 0.001 PHE F 377 TYR 0.013 0.001 TYR D 79 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 1) link_NAG-ASN : angle 0.70202 ( 3) link_BETA1-4 : bond 0.00486 ( 1) link_BETA1-4 : angle 1.01177 ( 3) hydrogen bonds : bond 0.03381 ( 112) hydrogen bonds : angle 6.48499 ( 270) link_BETA1-6 : bond 0.00362 ( 1) link_BETA1-6 : angle 1.27742 ( 3) SS BOND : bond 0.00576 ( 8) SS BOND : angle 1.23094 ( 16) covalent geometry : bond 0.00278 ( 6901) covalent geometry : angle 0.64284 ( 9381) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.7822 (m-80) cc_final: 0.7455 (m-10) REVERT: A 38 ARG cc_start: 0.8056 (ttp-170) cc_final: 0.7695 (ttp80) REVERT: A 96 CYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7511 (p) REVERT: B 38 GLN cc_start: 0.8030 (tt0) cc_final: 0.7579 (tt0) REVERT: B 55 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.7903 (mtp85) REVERT: H 78 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7618 (tp) REVERT: H 97 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6715 (mmm-85) REVERT: L 6 GLN cc_start: 0.6900 (pt0) cc_final: 0.6665 (pt0) REVERT: L 99 PHE cc_start: 0.8151 (m-80) cc_final: 0.7699 (m-10) REVERT: F 495 TYR cc_start: 0.8260 (m-80) cc_final: 0.7902 (m-80) REVERT: C 5 THR cc_start: 0.7244 (OUTLIER) cc_final: 0.6943 (p) REVERT: C 74 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7108 (mt) outliers start: 26 outliers final: 21 residues processed: 143 average time/residue: 0.2360 time to fit residues: 45.5319 Evaluate side-chains 148 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 20 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.0040 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.153493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.134696 restraints weight = 10429.138| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.05 r_work: 0.3682 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6912 Z= 0.124 Angle : 0.638 8.600 9406 Z= 0.326 Chirality : 0.043 0.237 1010 Planarity : 0.004 0.056 1207 Dihedral : 5.157 50.594 1024 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.96 % Favored : 87.92 % Rotamer: Outliers : 4.02 % Allowed : 25.90 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.11 (0.27), residues: 853 helix: -3.93 (1.12), residues: 14 sheet: -1.15 (0.32), residues: 287 loop : -2.69 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 50 HIS 0.006 0.001 HIS H 35 PHE 0.011 0.001 PHE F 377 TYR 0.013 0.001 TYR D 79 ARG 0.006 0.000 ARG A 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 1) link_NAG-ASN : angle 0.64613 ( 3) link_BETA1-4 : bond 0.00461 ( 1) link_BETA1-4 : angle 1.02494 ( 3) hydrogen bonds : bond 0.03394 ( 112) hydrogen bonds : angle 6.36027 ( 270) link_BETA1-6 : bond 0.00405 ( 1) link_BETA1-6 : angle 1.25980 ( 3) SS BOND : bond 0.00555 ( 8) SS BOND : angle 1.15637 ( 16) covalent geometry : bond 0.00282 ( 6901) covalent geometry : angle 0.63584 ( 9381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3877.00 seconds wall clock time: 69 minutes 8.73 seconds (4148.73 seconds total)