Starting phenix.real_space_refine on Wed Sep 17 15:43:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lbs_62955/09_2025/9lbs_62955.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lbs_62955/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9lbs_62955/09_2025/9lbs_62955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lbs_62955/09_2025/9lbs_62955.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lbs_62955/09_2025/9lbs_62955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lbs_62955/09_2025/9lbs_62955.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.82, per 1000 atoms: 0.27 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: 0.59 Conformation dependent library (CDL) restraints added in 356.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.20 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: 0.76 Time building geometry restraints manager: 0.80 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: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.960 Find NCS groups from input model: 0.050 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.160 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG F 454 TYR 0.021 0.001 TYR F 473 PHE 0.031 0.002 PHE D 67 TRP 0.079 0.003 TRP A 50 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 6901) covalent geometry : angle 0.75650 ( 9381) SS BOND : bond 0.00791 ( 8) SS BOND : angle 1.60420 ( 16) hydrogen bonds : bond 0.32914 ( 112) hydrogen bonds : angle 10.41253 ( 270) link_BETA1-4 : bond 0.04762 ( 1) link_BETA1-4 : angle 4.99030 ( 3) link_BETA1-6 : bond 0.03555 ( 1) link_BETA1-6 : angle 4.43315 ( 3) link_NAG-ASN : bond 0.00402 ( 1) link_NAG-ASN : angle 2.71442 ( 3) *********************** 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 : 0.238 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: 0.0913 time to fit residues: 15.1223 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 : 0.261 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.0570 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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** L 79 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN F 409 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.154129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.135647 restraints weight = 10303.506| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 3.01 r_work: 0.3699 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.0915 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= 0.120 Angle : 0.639 9.056 9406 Z= 0.331 Chirality : 0.043 0.164 1010 Planarity : 0.005 0.057 1207 Dihedral : 5.005 32.735 1025 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.49 % Favored : 88.39 % Rotamer: Outliers : 4.29 % Allowed : 23.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.26 (0.28), residues: 853 helix: -4.19 (0.82), residues: 21 sheet: -1.14 (0.34), residues: 272 loop : -2.79 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 53 TYR 0.012 0.001 TYR F 473 PHE 0.018 0.001 PHE F 456 TRP 0.036 0.002 TRP A 50 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6901) covalent geometry : angle 0.63797 ( 9381) SS BOND : bond 0.00276 ( 8) SS BOND : angle 0.77070 ( 16) hydrogen bonds : bond 0.04717 ( 112) hydrogen bonds : angle 7.79412 ( 270) link_BETA1-4 : bond 0.00366 ( 1) link_BETA1-4 : angle 1.00069 ( 3) link_BETA1-6 : bond 0.00485 ( 1) link_BETA1-6 : angle 1.27238 ( 3) link_NAG-ASN : bond 0.00410 ( 1) link_NAG-ASN : angle 0.44512 ( 3) *********************** 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 162 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 CYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7300 (p) REVERT: B 38 GLN cc_start: 0.7857 (tt0) cc_final: 0.7479 (tt0) REVERT: H 80 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7281 (tt) REVERT: L 6 GLN cc_start: 0.6681 (pt0) cc_final: 0.6417 (pt0) REVERT: L 99 PHE cc_start: 0.8079 (m-10) cc_final: 0.7715 (m-10) REVERT: D 5 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7853 (t) REVERT: C 74 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7291 (mt) outliers start: 31 outliers final: 13 residues processed: 151 average time/residue: 0.0800 time to fit residues: 16.5297 Evaluate side-chains 143 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 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 L residue 15 VAL Chi-restraints excluded: chain D residue 5 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 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 14 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.0670 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.152731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.134255 restraints weight = 10105.419| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.96 r_work: 0.3682 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6912 Z= 0.158 Angle : 0.648 8.956 9406 Z= 0.335 Chirality : 0.043 0.179 1010 Planarity : 0.005 0.056 1207 Dihedral : 5.083 35.562 1024 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.72 % Favored : 88.16 % Rotamer: Outliers : 5.26 % Allowed : 22.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.22 (0.27), residues: 853 helix: -4.06 (0.84), residues: 21 sheet: -1.13 (0.34), residues: 273 loop : -2.75 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 55 TYR 0.013 0.001 TYR L 32 PHE 0.014 0.001 PHE D 67 TRP 0.028 0.002 TRP A 50 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6901) covalent geometry : angle 0.64596 ( 9381) SS BOND : bond 0.00419 ( 8) SS BOND : angle 1.10827 ( 16) hydrogen bonds : bond 0.04606 ( 112) hydrogen bonds : angle 7.32098 ( 270) link_BETA1-4 : bond 0.00501 ( 1) link_BETA1-4 : angle 1.18323 ( 3) link_BETA1-6 : bond 0.00302 ( 1) link_BETA1-6 : angle 1.23519 ( 3) link_NAG-ASN : bond 0.00539 ( 1) link_NAG-ASN : angle 0.61902 ( 3) *********************** 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 165 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TRP cc_start: 0.8125 (t60) cc_final: 0.7922 (t60) REVERT: B 38 GLN cc_start: 0.8021 (tt0) cc_final: 0.7576 (tt0) REVERT: H 78 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7439 (tp) REVERT: H 80 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7412 (tt) REVERT: H 97 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6678 (mmm-85) REVERT: L 6 GLN cc_start: 0.6719 (pt0) cc_final: 0.6491 (pt0) REVERT: D 13 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8441 (mm-40) REVERT: C 5 THR cc_start: 0.7331 (OUTLIER) cc_final: 0.6971 (p) REVERT: C 74 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7273 (mt) outliers start: 38 outliers final: 24 residues processed: 152 average time/residue: 0.0741 time to fit residues: 15.4505 Evaluate side-chains 153 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 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 382 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 30 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 89 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.0000 chunk 50 optimal weight: 0.0370 chunk 26 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 1 optimal weight: 0.0570 overall best weight: 0.1978 ------------------------------------------------------------------------------- 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 F 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.155782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.136953 restraints weight = 10314.324| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.05 r_work: 0.3713 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6912 Z= 0.101 Angle : 0.602 8.504 9406 Z= 0.309 Chirality : 0.042 0.163 1010 Planarity : 0.004 0.055 1207 Dihedral : 4.872 38.531 1024 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.43 % Favored : 89.45 % Rotamer: Outliers : 5.40 % Allowed : 23.96 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.16 (0.28), residues: 853 helix: -4.14 (0.74), residues: 21 sheet: -1.14 (0.33), residues: 284 loop : -2.70 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.009 0.001 TYR F 351 PHE 0.011 0.001 PHE D 67 TRP 0.025 0.002 TRP A 36 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 6901) covalent geometry : angle 0.60054 ( 9381) SS BOND : bond 0.00329 ( 8) SS BOND : angle 0.95053 ( 16) hydrogen bonds : bond 0.03461 ( 112) hydrogen bonds : angle 6.88127 ( 270) link_BETA1-4 : bond 0.00399 ( 1) link_BETA1-4 : angle 1.03093 ( 3) link_BETA1-6 : bond 0.00366 ( 1) link_BETA1-6 : angle 1.31997 ( 3) link_NAG-ASN : bond 0.00413 ( 1) link_NAG-ASN : angle 0.44785 ( 3) *********************** 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 156 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 CYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7233 (p) REVERT: B 38 GLN cc_start: 0.7989 (tt0) cc_final: 0.7570 (tt0) REVERT: B 55 ARG cc_start: 0.8327 (mtp-110) cc_final: 0.8116 (mtp85) REVERT: H 78 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7448 (tp) REVERT: H 80 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7270 (tt) REVERT: L 99 PHE cc_start: 0.8112 (m-80) cc_final: 0.7747 (m-10) REVERT: D 50 VAL cc_start: 0.8669 (p) cc_final: 0.8298 (t) REVERT: C 5 THR cc_start: 0.7293 (OUTLIER) cc_final: 0.6937 (p) REVERT: C 74 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7216 (mt) outliers start: 39 outliers final: 21 residues processed: 148 average time/residue: 0.0776 time to fit residues: 15.7334 Evaluate side-chains 143 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 33 ASP 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 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 379 CYS 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 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 22 optimal weight: 0.0570 chunk 54 optimal weight: 0.0000 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.4102 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.154738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.135458 restraints weight = 10275.719| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.16 r_work: 0.3691 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.1573 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= 0.120 Angle : 0.609 8.454 9406 Z= 0.312 Chirality : 0.043 0.180 1010 Planarity : 0.004 0.055 1207 Dihedral : 4.891 39.941 1024 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.14 % Favored : 88.75 % Rotamer: Outliers : 5.12 % Allowed : 23.96 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.27), residues: 853 helix: -3.96 (0.86), residues: 21 sheet: -1.06 (0.33), residues: 282 loop : -2.70 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 403 TYR 0.010 0.001 TYR F 473 PHE 0.008 0.001 PHE C 61 TRP 0.031 0.002 TRP A 50 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6901) covalent geometry : angle 0.60810 ( 9381) SS BOND : bond 0.00422 ( 8) SS BOND : angle 0.88455 ( 16) hydrogen bonds : bond 0.03571 ( 112) hydrogen bonds : angle 6.71002 ( 270) link_BETA1-4 : bond 0.00474 ( 1) link_BETA1-4 : angle 1.04279 ( 3) link_BETA1-6 : bond 0.00274 ( 1) link_BETA1-6 : angle 1.25875 ( 3) link_NAG-ASN : bond 0.00479 ( 1) link_NAG-ASN : angle 0.54677 ( 3) *********************** 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 156 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 GLN cc_start: 0.8085 (tt0) cc_final: 0.7594 (tt0) REVERT: B 55 ARG cc_start: 0.8337 (mtp-110) cc_final: 0.8099 (mtp85) REVERT: H 80 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7394 (tt) REVERT: H 97 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6641 (mmm-85) REVERT: L 99 PHE cc_start: 0.8154 (m-80) cc_final: 0.7761 (m-10) REVERT: C 5 THR cc_start: 0.7306 (OUTLIER) cc_final: 0.6943 (p) REVERT: C 74 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7164 (mt) outliers start: 37 outliers final: 25 residues processed: 147 average time/residue: 0.0804 time to fit residues: 16.0462 Evaluate side-chains 148 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 96 CYS Chi-restraints excluded: chain A residue 110 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 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 D residue 17 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 357 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 0.0050 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 F 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.153462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.134410 restraints weight = 10385.144| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 3.12 r_work: 0.3682 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1631 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= 0.150 Angle : 0.629 8.622 9406 Z= 0.323 Chirality : 0.043 0.178 1010 Planarity : 0.004 0.055 1207 Dihedral : 5.021 42.143 1024 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.61 % Favored : 88.28 % Rotamer: Outliers : 4.99 % Allowed : 25.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.16 (0.27), residues: 853 helix: -3.83 (0.93), residues: 20 sheet: -1.09 (0.32), residues: 285 loop : -2.75 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 97 TYR 0.012 0.001 TYR F 473 PHE 0.011 0.001 PHE C 61 TRP 0.032 0.002 TRP A 50 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6901) covalent geometry : angle 0.62729 ( 9381) SS BOND : bond 0.00385 ( 8) SS BOND : angle 0.97791 ( 16) hydrogen bonds : bond 0.03795 ( 112) hydrogen bonds : angle 6.70762 ( 270) link_BETA1-4 : bond 0.00463 ( 1) link_BETA1-4 : angle 1.12561 ( 3) link_BETA1-6 : bond 0.00379 ( 1) link_BETA1-6 : angle 1.26273 ( 3) link_NAG-ASN : bond 0.00566 ( 1) link_NAG-ASN : angle 0.61571 ( 3) *********************** 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 156 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 GLN cc_start: 0.8102 (tt0) cc_final: 0.7621 (tt0) REVERT: B 55 ARG cc_start: 0.8354 (mtp-110) cc_final: 0.8118 (mtp85) REVERT: H 97 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6701 (mmm-85) REVERT: L 99 PHE cc_start: 0.8164 (m-80) cc_final: 0.7761 (m-10) REVERT: C 5 THR cc_start: 0.7307 (OUTLIER) cc_final: 0.6956 (p) REVERT: C 74 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7175 (mt) outliers start: 36 outliers final: 29 residues processed: 145 average time/residue: 0.0819 time to fit residues: 16.0847 Evaluate side-chains 150 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 B residue 92 HIS Chi-restraints excluded: chain B residue 104 VAL 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 357 ARG 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 20 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 76 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 21 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.152298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.133158 restraints weight = 10290.203| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.10 r_work: 0.3665 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1700 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= 0.178 Angle : 0.658 8.475 9406 Z= 0.337 Chirality : 0.044 0.187 1010 Planarity : 0.005 0.056 1207 Dihedral : 5.168 44.664 1024 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.66 % Favored : 87.22 % Rotamer: Outliers : 5.54 % Allowed : 24.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.20 (0.27), residues: 853 helix: -3.89 (0.87), residues: 20 sheet: -1.19 (0.32), residues: 296 loop : -2.76 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 97 TYR 0.022 0.001 TYR A 32 PHE 0.013 0.001 PHE C 61 TRP 0.035 0.002 TRP A 50 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 6901) covalent geometry : angle 0.65603 ( 9381) SS BOND : bond 0.00529 ( 8) SS BOND : angle 1.33965 ( 16) hydrogen bonds : bond 0.04011 ( 112) hydrogen bonds : angle 6.74632 ( 270) link_BETA1-4 : bond 0.00506 ( 1) link_BETA1-4 : angle 1.18161 ( 3) link_BETA1-6 : bond 0.00379 ( 1) link_BETA1-6 : angle 1.29217 ( 3) link_NAG-ASN : bond 0.00622 ( 1) link_NAG-ASN : angle 0.72155 ( 3) *********************** 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 165 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 GLN cc_start: 0.8133 (tt0) cc_final: 0.7631 (tt0) REVERT: B 55 ARG cc_start: 0.8369 (mtp-110) cc_final: 0.8114 (mtp85) REVERT: H 51 ILE cc_start: 0.8212 (tp) cc_final: 0.7997 (tp) REVERT: H 80 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7495 (tt) REVERT: H 97 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6739 (mmm-85) REVERT: L 99 PHE cc_start: 0.8178 (m-80) cc_final: 0.7752 (m-10) REVERT: D 50 VAL cc_start: 0.8670 (p) cc_final: 0.8386 (t) REVERT: C 5 THR cc_start: 0.7274 (OUTLIER) cc_final: 0.6943 (p) REVERT: C 74 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7166 (mt) outliers start: 40 outliers final: 27 residues processed: 152 average time/residue: 0.0784 time to fit residues: 16.1749 Evaluate side-chains 155 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 92 HIS Chi-restraints excluded: chain B residue 104 VAL 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 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 D residue 17 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 20 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 D 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.152157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.133084 restraints weight = 10386.184| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.15 r_work: 0.3654 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1788 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= 0.179 Angle : 0.665 8.603 9406 Z= 0.343 Chirality : 0.044 0.199 1010 Planarity : 0.005 0.056 1207 Dihedral : 5.302 46.809 1024 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.19 % Favored : 87.69 % Rotamer: Outliers : 5.12 % Allowed : 24.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.23 (0.27), residues: 853 helix: -3.88 (0.87), residues: 20 sheet: -1.19 (0.32), residues: 292 loop : -2.78 (0.23), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.023 0.001 TYR A 32 PHE 0.013 0.001 PHE C 61 TRP 0.038 0.003 TRP A 50 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 6901) covalent geometry : angle 0.66282 ( 9381) SS BOND : bond 0.00516 ( 8) SS BOND : angle 1.16288 ( 16) hydrogen bonds : bond 0.04027 ( 112) hydrogen bonds : angle 6.75478 ( 270) link_BETA1-4 : bond 0.00444 ( 1) link_BETA1-4 : angle 1.18311 ( 3) link_BETA1-6 : bond 0.00611 ( 1) link_BETA1-6 : angle 1.32682 ( 3) link_NAG-ASN : bond 0.00629 ( 1) link_NAG-ASN : angle 0.81967 ( 3) *********************** 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 162 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 GLN cc_start: 0.8145 (tt0) cc_final: 0.7639 (tt0) REVERT: B 55 ARG cc_start: 0.8379 (mtp-110) cc_final: 0.8094 (mtp85) REVERT: H 51 ILE cc_start: 0.8259 (tp) cc_final: 0.8041 (tp) REVERT: H 80 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7534 (tt) REVERT: H 97 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6729 (mmm-85) REVERT: L 6 GLN cc_start: 0.6855 (pt0) cc_final: 0.6474 (pt0) REVERT: D 50 VAL cc_start: 0.8662 (p) cc_final: 0.8380 (t) REVERT: C 5 THR cc_start: 0.7271 (OUTLIER) cc_final: 0.6941 (p) REVERT: C 74 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7124 (mt) outliers start: 37 outliers final: 27 residues processed: 149 average time/residue: 0.0857 time to fit residues: 17.1738 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 : 0.243 ------------------------------------------------------------------------------- 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 B residue 92 HIS Chi-restraints excluded: chain B residue 104 VAL 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 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 D residue 17 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 357 ARG 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 20 ILE 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 6 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 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 A 116 ASN B 6 GLN D 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.152360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.133126 restraints weight = 10339.961| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.16 r_work: 0.3659 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1857 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= 0.161 Angle : 0.665 8.674 9406 Z= 0.342 Chirality : 0.044 0.211 1010 Planarity : 0.005 0.073 1207 Dihedral : 5.331 48.145 1024 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.08 % Favored : 87.81 % Rotamer: Outliers : 4.99 % Allowed : 24.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.19 (0.27), residues: 853 helix: -3.84 (0.90), residues: 20 sheet: -1.12 (0.32), residues: 286 loop : -2.77 (0.23), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.026 0.001 TYR A 32 PHE 0.021 0.001 PHE F 456 TRP 0.050 0.003 TRP A 50 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6901) covalent geometry : angle 0.66311 ( 9381) SS BOND : bond 0.00483 ( 8) SS BOND : angle 1.07209 ( 16) hydrogen bonds : bond 0.03854 ( 112) hydrogen bonds : angle 6.75090 ( 270) link_BETA1-4 : bond 0.00433 ( 1) link_BETA1-4 : angle 1.11695 ( 3) link_BETA1-6 : bond 0.00353 ( 1) link_BETA1-6 : angle 1.27443 ( 3) link_NAG-ASN : bond 0.00591 ( 1) link_NAG-ASN : angle 0.82436 ( 3) *********************** 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 164 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 GLN cc_start: 0.8141 (tt0) cc_final: 0.7634 (tt0) REVERT: B 55 ARG cc_start: 0.8371 (mtp-110) cc_final: 0.8090 (mtp85) REVERT: H 51 ILE cc_start: 0.8292 (tp) cc_final: 0.8074 (tp) REVERT: H 80 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7509 (tt) REVERT: H 97 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6716 (mmm-85) REVERT: D 50 VAL cc_start: 0.8666 (p) cc_final: 0.8375 (t) REVERT: C 5 THR cc_start: 0.7271 (OUTLIER) cc_final: 0.6948 (p) REVERT: C 74 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7134 (mt) outliers start: 36 outliers final: 27 residues processed: 151 average time/residue: 0.0824 time to fit residues: 16.8117 Evaluate side-chains 158 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 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 48 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 104 VAL 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 20 optimal weight: 0.0970 chunk 39 optimal weight: 7.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.152992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.134421 restraints weight = 10313.068| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.98 r_work: 0.3687 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1921 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= 0.143 Angle : 0.648 8.730 9406 Z= 0.335 Chirality : 0.043 0.214 1010 Planarity : 0.005 0.056 1207 Dihedral : 5.298 49.184 1024 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.84 % Favored : 88.04 % Rotamer: Outliers : 4.57 % Allowed : 25.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.16 (0.27), residues: 853 helix: -3.81 (0.93), residues: 20 sheet: -1.12 (0.32), residues: 290 loop : -2.75 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.016 0.001 TYR A 32 PHE 0.019 0.001 PHE F 456 TRP 0.069 0.003 TRP A 50 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6901) covalent geometry : angle 0.64708 ( 9381) SS BOND : bond 0.00453 ( 8) SS BOND : angle 1.02281 ( 16) hydrogen bonds : bond 0.03645 ( 112) hydrogen bonds : angle 6.69507 ( 270) link_BETA1-4 : bond 0.00383 ( 1) link_BETA1-4 : angle 1.05765 ( 3) link_BETA1-6 : bond 0.00385 ( 1) link_BETA1-6 : angle 1.27741 ( 3) link_NAG-ASN : bond 0.00551 ( 1) link_NAG-ASN : angle 0.79945 ( 3) ********************** 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 156 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 GLN cc_start: 0.8051 (tt0) cc_final: 0.7612 (tt0) REVERT: B 55 ARG cc_start: 0.8360 (mtp-110) cc_final: 0.8156 (mtp85) REVERT: H 51 ILE cc_start: 0.8266 (tp) cc_final: 0.8052 (tp) REVERT: H 97 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6704 (mmm-85) REVERT: L 6 GLN cc_start: 0.6821 (pt0) cc_final: 0.6473 (pt0) REVERT: L 99 PHE cc_start: 0.8123 (m-80) cc_final: 0.7743 (m-10) REVERT: D 50 VAL cc_start: 0.8675 (p) cc_final: 0.8387 (t) REVERT: C 5 THR cc_start: 0.7291 (OUTLIER) cc_final: 0.6979 (p) REVERT: C 74 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7209 (mt) outliers start: 33 outliers final: 28 residues processed: 147 average time/residue: 0.0866 time to fit residues: 17.1027 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 : 0.251 ------------------------------------------------------------------------------- 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 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 48 LEU Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 104 VAL 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 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 357 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 22 optimal weight: 0.0470 chunk 2 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.152590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.133638 restraints weight = 10322.386| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.08 r_work: 0.3676 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.2000 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= 0.152 Angle : 0.658 8.664 9406 Z= 0.338 Chirality : 0.044 0.219 1010 Planarity : 0.005 0.056 1207 Dihedral : 5.298 49.438 1024 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.08 % Favored : 87.81 % Rotamer: Outliers : 3.74 % Allowed : 26.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.15 (0.27), residues: 853 helix: -3.83 (0.91), residues: 20 sheet: -1.14 (0.32), residues: 292 loop : -2.73 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 98 TYR 0.015 0.001 TYR D 79 PHE 0.019 0.001 PHE F 456 TRP 0.084 0.003 TRP A 50 HIS 0.009 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6901) covalent geometry : angle 0.65708 ( 9381) SS BOND : bond 0.00439 ( 8) SS BOND : angle 1.03289 ( 16) hydrogen bonds : bond 0.03653 ( 112) hydrogen bonds : angle 6.64445 ( 270) link_BETA1-4 : bond 0.00450 ( 1) link_BETA1-4 : angle 1.08452 ( 3) link_BETA1-6 : bond 0.00400 ( 1) link_BETA1-6 : angle 1.25900 ( 3) link_NAG-ASN : bond 0.00567 ( 1) link_NAG-ASN : angle 0.79941 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1757.48 seconds wall clock time: 30 minutes 50.86 seconds (1850.86 seconds total)