Starting phenix.real_space_refine on Tue May 13 00:02:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lbs_62955/05_2025/9lbs_62955.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lbs_62955/05_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_62955/05_2025/9lbs_62955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lbs_62955/05_2025/9lbs_62955.map" model { file = "/net/cci-nas-00/data/ceres_data/9lbs_62955/05_2025/9lbs_62955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lbs_62955/05_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-5687/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: 5.11, per 1000 atoms: 0.76 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: 1.78 Conformation dependent library (CDL) restraints added in 953.2 milliseconds 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: 0.89 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: 1.56 Time building geometry restraints manager: 2.03 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: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.700 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.820 ------------------------------------------------------------------------------- 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 : 0.662 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: 0.1999 time to fit residues: 32.4620 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 : 0.657 ------------------------------------------------------------------------------- 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 = 0.151705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132658 restraints weight = 10208.597| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.12 r_work: 0.3651 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- 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 0.60187 ( 3) link_BETA1-4 : bond 0.00555 ( 1) link_BETA1-4 : angle 1.35202 ( 3) hydrogen bonds : bond 0.05426 ( 112) hydrogen bonds : angle 7.78717 ( 270) link_BETA1-6 : bond 0.00657 ( 1) link_BETA1-6 : angle 1.32894 ( 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 : 0.720 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: 0.8055 (tt0) cc_final: 0.7591 (tt0) REVERT: H 80 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7437 (tt) REVERT: H 97 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6724 (mmm-85) REVERT: L 6 GLN cc_start: 0.6894 (pt0) cc_final: 0.6626 (pt0) REVERT: D 13 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8421 (mm-40) REVERT: C 74 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7257 (mt) outliers start: 38 outliers final: 22 residues processed: 151 average time/residue: 0.1665 time to fit residues: 34.1824 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 : 0.656 ------------------------------------------------------------------------------- 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: 0.5980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4048 r_free = 0.4048 target = 0.152380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.133984 restraints weight = 10210.707| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.98 r_work: 0.3674 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6912 Z= 0.149 Angle : 0.650 8.919 9406 Z= 0.336 Chirality : 0.043 0.178 1010 Planarity : 0.005 0.057 1207 Dihedral : 5.240 38.352 1024 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.19 % Favored : 87.69 % 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: -3.29 (0.27), residues: 853 helix: -3.99 (0.87), residues: 21 sheet: -1.24 (0.33), residues: 279 loop : -2.79 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.014 0.001 PHE D 67 TYR 0.011 0.001 TYR L 32 ARG 0.002 0.000 ARG B 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 1) link_NAG-ASN : angle 0.59144 ( 3) link_BETA1-4 : bond 0.00663 ( 1) link_BETA1-4 : angle 1.11508 ( 3) hydrogen bonds : bond 0.04511 ( 112) hydrogen bonds : angle 7.30104 ( 270) link_BETA1-6 : bond 0.00461 ( 1) link_BETA1-6 : angle 1.29700 ( 3) SS BOND : bond 0.00445 ( 8) SS BOND : angle 1.05598 ( 16) covalent geometry : bond 0.00340 ( 6901) covalent geometry : angle 0.64842 ( 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 162 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TRP cc_start: 0.8097 (t60) cc_final: 0.7801 (t60) REVERT: A 96 CYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7244 (p) REVERT: B 38 GLN cc_start: 0.8007 (tt0) cc_final: 0.7551 (tt0) REVERT: H 78 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7414 (tp) REVERT: H 97 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6718 (mmm-85) REVERT: L 6 GLN cc_start: 0.6832 (pt0) cc_final: 0.6603 (pt0) REVERT: L 99 PHE cc_start: 0.8153 (m-80) cc_final: 0.7771 (m-10) REVERT: D 13 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8452 (mm-40) REVERT: C 5 THR cc_start: 0.7297 (OUTLIER) cc_final: 0.6945 (p) REVERT: C 74 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7257 (mt) outliers start: 35 outliers final: 19 residues processed: 151 average time/residue: 0.1782 time to fit residues: 36.1047 Evaluate side-chains 150 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 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 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: 0.4980 chunk 79 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 0.0030 chunk 70 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 overall best weight: 0.3388 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.154308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.135136 restraints weight = 10316.418| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 3.14 r_work: 0.3686 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6912 Z= 0.114 Angle : 0.611 8.950 9406 Z= 0.317 Chirality : 0.042 0.163 1010 Planarity : 0.004 0.056 1207 Dihedral : 5.069 40.539 1024 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.49 % Favored : 88.39 % Rotamer: Outliers : 5.54 % Allowed : 24.38 % 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: -3.22 (0.27), residues: 853 helix: -3.98 (0.83), residues: 20 sheet: -1.23 (0.32), residues: 289 loop : -2.74 (0.24), residues: 544 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 0.012 0.001 TYR F 351 ARG 0.002 0.000 ARG F 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 1) link_NAG-ASN : angle 0.49406 ( 3) link_BETA1-4 : bond 0.00565 ( 1) link_BETA1-4 : angle 1.00889 ( 3) hydrogen bonds : bond 0.03684 ( 112) hydrogen bonds : angle 6.90078 ( 270) link_BETA1-6 : bond 0.00405 ( 1) link_BETA1-6 : angle 1.29478 ( 3) SS BOND : bond 0.00489 ( 8) SS BOND : angle 0.96380 ( 16) covalent geometry : bond 0.00259 ( 6901) covalent geometry : angle 0.60979 ( 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 164 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TRP cc_start: 0.8025 (t60) cc_final: 0.7810 (t60) REVERT: A 96 CYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7280 (p) REVERT: B 38 GLN cc_start: 0.8021 (tt0) cc_final: 0.7551 (tt0) REVERT: B 55 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.8069 (mtp85) REVERT: H 78 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7519 (tp) REVERT: H 80 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7330 (tt) REVERT: H 97 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6701 (mmm-85) REVERT: L 99 PHE cc_start: 0.8168 (m-80) cc_final: 0.7779 (m-10) REVERT: D 13 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8522 (mm-40) REVERT: C 5 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.6973 (p) REVERT: C 74 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7151 (mt) outliers start: 40 outliers final: 25 residues processed: 153 average time/residue: 0.1619 time to fit residues: 33.7777 Evaluate side-chains 154 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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 31 SER Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 37 VAL 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: 0.9990 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 F 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.152217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133085 restraints weight = 10145.001| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.08 r_work: 0.3657 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1582 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= 0.175 Angle : 0.652 8.814 9406 Z= 0.335 Chirality : 0.044 0.184 1010 Planarity : 0.005 0.057 1207 Dihedral : 5.244 43.679 1024 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.19 % Favored : 87.69 % Rotamer: Outliers : 5.40 % Allowed : 24.52 % 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: -3.29 (0.27), residues: 853 helix: -3.89 (0.88), residues: 20 sheet: -1.35 (0.32), residues: 296 loop : -2.75 (0.24), residues: 537 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 0.013 0.001 PHE C 61 TYR 0.014 0.001 TYR L 32 ARG 0.002 0.000 ARG B 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 1) link_NAG-ASN : angle 0.65347 ( 3) link_BETA1-4 : bond 0.00441 ( 1) link_BETA1-4 : angle 1.18273 ( 3) hydrogen bonds : bond 0.04169 ( 112) hydrogen bonds : angle 6.85781 ( 270) link_BETA1-6 : bond 0.00424 ( 1) link_BETA1-6 : angle 1.26000 ( 3) SS BOND : bond 0.00514 ( 8) SS BOND : angle 1.15764 ( 16) covalent geometry : bond 0.00397 ( 6901) covalent geometry : angle 0.64996 ( 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 167 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TRP cc_start: 0.8082 (t60) cc_final: 0.7740 (t60) REVERT: B 38 GLN cc_start: 0.8081 (tt0) cc_final: 0.7748 (tt0) REVERT: B 55 ARG cc_start: 0.8362 (mtp-110) cc_final: 0.8077 (mtp85) REVERT: H 78 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7469 (tp) REVERT: H 97 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6814 (mmm-85) REVERT: L 99 PHE cc_start: 0.8205 (m-80) cc_final: 0.7777 (m-10) REVERT: C 5 THR cc_start: 0.7283 (OUTLIER) cc_final: 0.6949 (p) REVERT: C 74 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7141 (mt) outliers start: 39 outliers final: 28 residues processed: 157 average time/residue: 0.1748 time to fit residues: 37.0032 Evaluate side-chains 155 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 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 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 31 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 408 SER Chi-restraints excluded: chain F residue 433 VAL 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: 6.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 0.0070 chunk 21 optimal weight: 0.0010 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 71 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 overall best weight: 0.0582 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.156154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.136801 restraints weight = 10210.115| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.19 r_work: 0.3706 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6912 Z= 0.101 Angle : 0.614 9.324 9406 Z= 0.314 Chirality : 0.043 0.160 1010 Planarity : 0.004 0.056 1207 Dihedral : 4.982 44.930 1024 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.43 % Favored : 89.45 % Rotamer: Outliers : 4.43 % Allowed : 25.62 % 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: -3.13 (0.27), residues: 853 helix: -3.99 (0.82), residues: 20 sheet: -1.05 (0.33), residues: 281 loop : -2.73 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE F 456 TYR 0.014 0.001 TYR D 79 ARG 0.002 0.000 ARG H 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 1) link_NAG-ASN : angle 0.53314 ( 3) link_BETA1-4 : bond 0.00331 ( 1) link_BETA1-4 : angle 1.01480 ( 3) hydrogen bonds : bond 0.03147 ( 112) hydrogen bonds : angle 6.57387 ( 270) link_BETA1-6 : bond 0.00267 ( 1) link_BETA1-6 : angle 1.31312 ( 3) SS BOND : bond 0.00483 ( 8) SS BOND : angle 1.04223 ( 16) covalent geometry : bond 0.00218 ( 6901) covalent geometry : angle 0.61274 ( 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 146 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7956 (ttp-170) cc_final: 0.7590 (ttp80) REVERT: A 96 CYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7570 (p) REVERT: B 38 GLN cc_start: 0.8066 (tt0) cc_final: 0.7575 (tt0) REVERT: B 55 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.8050 (mtp85) REVERT: L 99 PHE cc_start: 0.8111 (m-80) cc_final: 0.7694 (m-10) REVERT: C 5 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.6952 (p) REVERT: C 74 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7066 (mt) outliers start: 32 outliers final: 21 residues processed: 138 average time/residue: 0.1818 time to fit residues: 33.8036 Evaluate side-chains 137 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 124 THR Chi-restraints excluded: chain B residue 28 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 35 HIS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR 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 37 VAL Chi-restraints excluded: chain D residue 78 LEU 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: 0.5980 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN F 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.150702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.131592 restraints weight = 10271.902| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.08 r_work: 0.3639 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6912 Z= 0.227 Angle : 0.698 8.578 9406 Z= 0.360 Chirality : 0.045 0.211 1010 Planarity : 0.005 0.055 1207 Dihedral : 5.395 47.648 1024 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.13 % Favored : 86.75 % Rotamer: Outliers : 4.99 % Allowed : 24.93 % 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: -3.23 (0.27), residues: 853 helix: -4.03 (1.04), residues: 14 sheet: -1.27 (0.31), residues: 297 loop : -2.76 (0.23), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 50 HIS 0.007 0.002 HIS H 35 PHE 0.016 0.002 PHE C 61 TYR 0.020 0.002 TYR L 32 ARG 0.002 0.000 ARG F 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00730 ( 1) link_NAG-ASN : angle 0.77184 ( 3) link_BETA1-4 : bond 0.00456 ( 1) link_BETA1-4 : angle 1.47452 ( 3) hydrogen bonds : bond 0.04396 ( 112) hydrogen bonds : angle 6.76030 ( 270) link_BETA1-6 : bond 0.00504 ( 1) link_BETA1-6 : angle 1.30967 ( 3) SS BOND : bond 0.00540 ( 8) SS BOND : angle 1.28766 ( 16) covalent geometry : bond 0.00514 ( 6901) covalent geometry : angle 0.69556 ( 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 159 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 TRP cc_start: 0.8247 (t60) cc_final: 0.7984 (t60) REVERT: B 38 GLN cc_start: 0.8126 (tt0) cc_final: 0.7652 (tt0) REVERT: B 55 ARG cc_start: 0.8372 (mtp-110) cc_final: 0.8074 (mtp85) REVERT: H 51 ILE cc_start: 0.8355 (tp) cc_final: 0.8140 (tp) REVERT: H 97 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6889 (mmm-85) REVERT: L 6 GLN cc_start: 0.6775 (pt0) cc_final: 0.6509 (pt0) REVERT: L 99 PHE cc_start: 0.8229 (m-80) cc_final: 0.7804 (m-10) REVERT: C 5 THR cc_start: 0.7311 (OUTLIER) cc_final: 0.7027 (p) REVERT: C 74 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7110 (mt) outliers start: 36 outliers final: 28 residues processed: 150 average time/residue: 0.1813 time to fit residues: 36.5540 Evaluate side-chains 152 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 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 35 HIS Chi-restraints excluded: chain H residue 45 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 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 D 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.151725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132684 restraints weight = 10245.303| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 3.07 r_work: 0.3650 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.1917 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= 0.172 Angle : 0.661 8.623 9406 Z= 0.341 Chirality : 0.044 0.193 1010 Planarity : 0.005 0.056 1207 Dihedral : 5.427 49.748 1024 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.84 % Favored : 88.04 % Rotamer: Outliers : 4.85 % Allowed : 25.62 % 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: -3.25 (0.27), residues: 853 helix: -3.80 (1.24), residues: 14 sheet: -1.27 (0.31), residues: 296 loop : -2.79 (0.23), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 50 HIS 0.007 0.002 HIS H 35 PHE 0.013 0.001 PHE C 61 TYR 0.019 0.002 TYR A 32 ARG 0.004 0.000 ARG D 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 1) link_NAG-ASN : angle 0.81113 ( 3) link_BETA1-4 : bond 0.00479 ( 1) link_BETA1-4 : angle 1.14456 ( 3) hydrogen bonds : bond 0.03980 ( 112) hydrogen bonds : angle 6.71667 ( 270) link_BETA1-6 : bond 0.00480 ( 1) link_BETA1-6 : angle 1.28550 ( 3) SS BOND : bond 0.00450 ( 8) SS BOND : angle 1.05265 ( 16) covalent geometry : bond 0.00388 ( 6901) covalent geometry : angle 0.65920 ( 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 156 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 TRP cc_start: 0.8213 (t60) cc_final: 0.7903 (t60) REVERT: B 38 GLN cc_start: 0.8100 (tt0) cc_final: 0.7641 (tt0) REVERT: B 55 ARG cc_start: 0.8365 (mtp-110) cc_final: 0.8087 (mtp85) REVERT: H 51 ILE cc_start: 0.8346 (tp) cc_final: 0.8131 (tp) REVERT: H 97 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6808 (mmm-85) REVERT: L 6 GLN cc_start: 0.6862 (pt0) cc_final: 0.6602 (pt0) REVERT: C 5 THR cc_start: 0.7276 (OUTLIER) cc_final: 0.6976 (p) REVERT: C 74 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7132 (mt) outliers start: 35 outliers final: 26 residues processed: 146 average time/residue: 0.1803 time to fit residues: 35.3169 Evaluate side-chains 150 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 92 HIS Chi-restraints excluded: chain H residue 18 LEU 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 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 31 SER Chi-restraints excluded: chain D residue 32 ASN 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 46 VAL 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: 1.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 6 GLN D 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.151831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132517 restraints weight = 10331.369| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.15 r_work: 0.3653 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6912 Z= 0.162 Angle : 0.669 9.777 9406 Z= 0.345 Chirality : 0.044 0.220 1010 Planarity : 0.005 0.056 1207 Dihedral : 5.413 50.109 1024 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.43 % Favored : 87.46 % Rotamer: Outliers : 4.57 % Allowed : 25.21 % 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: -3.18 (0.27), residues: 853 helix: -3.85 (1.19), residues: 14 sheet: -1.13 (0.32), residues: 289 loop : -2.78 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 50 HIS 0.006 0.002 HIS H 35 PHE 0.011 0.001 PHE C 61 TYR 0.017 0.001 TYR A 32 ARG 0.005 0.000 ARG D 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 1) link_NAG-ASN : angle 0.81128 ( 3) link_BETA1-4 : bond 0.00290 ( 1) link_BETA1-4 : angle 1.13954 ( 3) hydrogen bonds : bond 0.03844 ( 112) hydrogen bonds : angle 6.67630 ( 270) link_BETA1-6 : bond 0.00344 ( 1) link_BETA1-6 : angle 1.25609 ( 3) SS BOND : bond 0.00553 ( 8) SS BOND : angle 1.43570 ( 16) covalent geometry : bond 0.00368 ( 6901) covalent geometry : angle 0.66690 ( 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: 33 poor density : 123 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 TRP cc_start: 0.8207 (t60) cc_final: 0.7839 (t60) REVERT: B 38 GLN cc_start: 0.8112 (tt0) cc_final: 0.7641 (tt0) REVERT: B 55 ARG cc_start: 0.8356 (mtp-110) cc_final: 0.8073 (mtp85) REVERT: H 51 ILE cc_start: 0.8371 (tp) cc_final: 0.8158 (tp) REVERT: H 97 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6796 (mmm-85) REVERT: L 6 GLN cc_start: 0.6900 (pt0) cc_final: 0.6637 (pt0) REVERT: C 5 THR cc_start: 0.7272 (OUTLIER) cc_final: 0.6967 (p) REVERT: C 74 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7117 (mt) outliers start: 33 outliers final: 27 residues processed: 144 average time/residue: 0.1983 time to fit residues: 38.0715 Evaluate side-chains 152 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 64 PHE 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 48 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 104 VAL 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 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 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: 1.9990 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 27 optimal weight: 0.0370 chunk 65 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 116 ASN 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 = 0.152418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.133620 restraints weight = 10362.061| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.02 r_work: 0.3668 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2065 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= 0.150 Angle : 0.658 9.059 9406 Z= 0.339 Chirality : 0.043 0.213 1010 Planarity : 0.005 0.056 1207 Dihedral : 5.371 50.088 1024 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.61 % Favored : 88.28 % Rotamer: Outliers : 4.43 % Allowed : 25.48 % 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: -3.19 (0.27), residues: 853 helix: -3.90 (1.15), residues: 14 sheet: -1.19 (0.32), residues: 290 loop : -2.76 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 50 HIS 0.006 0.002 HIS H 35 PHE 0.010 0.001 PHE F 377 TYR 0.016 0.001 TYR A 32 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 1) link_NAG-ASN : angle 0.77583 ( 3) link_BETA1-4 : bond 0.00453 ( 1) link_BETA1-4 : angle 1.07086 ( 3) hydrogen bonds : bond 0.03661 ( 112) hydrogen bonds : angle 6.62583 ( 270) link_BETA1-6 : bond 0.00405 ( 1) link_BETA1-6 : angle 1.25554 ( 3) SS BOND : bond 0.00617 ( 8) SS BOND : angle 1.31652 ( 16) covalent geometry : bond 0.00341 ( 6901) covalent geometry : angle 0.65589 ( 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 155 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 TRP cc_start: 0.8164 (t60) cc_final: 0.7752 (t60) REVERT: A 96 CYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7566 (p) REVERT: B 38 GLN cc_start: 0.8038 (tt0) cc_final: 0.7628 (tt0) REVERT: B 55 ARG cc_start: 0.8338 (mtp-110) cc_final: 0.7964 (mtp180) REVERT: H 51 ILE cc_start: 0.8369 (tp) cc_final: 0.8156 (tp) REVERT: H 97 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6783 (mmm-85) REVERT: L 6 GLN cc_start: 0.6927 (pt0) cc_final: 0.6670 (pt0) REVERT: L 99 PHE cc_start: 0.8153 (m-80) cc_final: 0.7745 (m-10) REVERT: C 5 THR cc_start: 0.7274 (OUTLIER) cc_final: 0.6975 (p) REVERT: C 74 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7155 (mt) outliers start: 32 outliers final: 27 residues processed: 147 average time/residue: 0.1881 time to fit residues: 37.3370 Evaluate side-chains 153 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 64 PHE 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 48 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 104 VAL 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 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 78 LEU 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 75 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.153139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.134014 restraints weight = 10482.900| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 3.06 r_work: 0.3675 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6912 Z= 0.135 Angle : 0.649 8.972 9406 Z= 0.334 Chirality : 0.044 0.226 1010 Planarity : 0.004 0.057 1207 Dihedral : 5.301 50.488 1024 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.96 % Favored : 87.92 % Rotamer: Outliers : 3.88 % Allowed : 26.18 % 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 (1.13), residues: 14 sheet: -1.14 (0.32), residues: 288 loop : -2.73 (0.23), residues: 551 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 0.014 0.001 PHE F 377 TYR 0.013 0.001 TYR A 32 ARG 0.005 0.000 ARG A 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 1) link_NAG-ASN : angle 0.69608 ( 3) link_BETA1-4 : bond 0.00433 ( 1) link_BETA1-4 : angle 1.04977 ( 3) hydrogen bonds : bond 0.03515 ( 112) hydrogen bonds : angle 6.55063 ( 270) link_BETA1-6 : bond 0.00262 ( 1) link_BETA1-6 : angle 1.23160 ( 3) SS BOND : bond 0.00578 ( 8) SS BOND : angle 1.22018 ( 16) covalent geometry : bond 0.00310 ( 6901) covalent geometry : angle 0.64733 ( 9381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3220.80 seconds wall clock time: 56 minutes 44.46 seconds (3404.46 seconds total)