Starting phenix.real_space_refine on Fri Aug 22 13:13:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hzc_35088/08_2025/8hzc_35088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hzc_35088/08_2025/8hzc_35088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hzc_35088/08_2025/8hzc_35088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hzc_35088/08_2025/8hzc_35088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hzc_35088/08_2025/8hzc_35088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hzc_35088/08_2025/8hzc_35088.map" } resolution = 3.2 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1938 2.51 5 N 546 2.21 5 O 624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3108 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 518 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Restraints were copied for chains: D, E, F, B, C Time building chain proxies: 0.54, per 1000 atoms: 0.17 Number of scatterers: 3108 At special positions: 0 Unit cell: (103.75, 112.05, 34.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 624 8.00 N 546 7.00 C 1938 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.14 Conformation dependent library (CDL) restraints added in 76.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 57.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 15 through 24 removed outlier: 6.359A pdb=" N VAL A 16 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ALA E 19 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA A 18 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LYS E 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU A 20 " --> pdb=" O LYS E 21 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LYS E 23 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR A 22 " --> pdb=" O LYS E 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 45 through 49 removed outlier: 5.594A pdb=" N GLU A 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N VAL D 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU E 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY A 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 52 through 56 Processing sheet with id=AA4, first strand: chain 'D' and resid 61 through 66 removed outlier: 6.520A pdb=" N GLN A 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ASN D 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR A 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 82 removed outlier: 6.912A pdb=" N VAL A 70 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL D 71 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR A 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY D 73 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL D 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN D 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS A 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR D 81 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ALA A 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N THR E 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N VAL A 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N VAL E 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA E 76 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N THR A 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA E 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N VAL A 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 10.822A pdb=" N LYS E 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N GLN A 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 10.348A pdb=" N VAL E 82 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N THR A 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 87 through 92 removed outlier: 6.839A pdb=" N ILE D 88 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE A 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA E 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 95 through 98 removed outlier: 6.433A pdb=" N LYS A 96 " --> pdb=" O LYS D 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 15 through 24 removed outlier: 6.359A pdb=" N VAL F 16 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ALA C 19 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA F 18 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LYS C 21 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU F 20 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LYS C 23 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR F 22 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 49 removed outlier: 5.595A pdb=" N GLU F 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N VAL B 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL F 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU C 46 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY F 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 66 removed outlier: 6.520A pdb=" N GLN F 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ASN B 65 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR F 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 82 removed outlier: 6.911A pdb=" N VAL F 70 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 71 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR F 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY B 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA F 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN B 79 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS F 80 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR B 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL F 82 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ALA F 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N THR C 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N VAL F 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N VAL C 74 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY F 73 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA C 76 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N THR F 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA C 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N VAL F 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N LYS C 80 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N GLN F 79 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL C 82 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N THR F 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 87 through 92 removed outlier: 6.839A pdb=" N ILE B 88 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE F 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA C 91 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA F 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 95 through 98 removed outlier: 6.432A pdb=" N LYS F 96 " --> pdb=" O LYS B 97 " (cutoff:3.500A) 68 hydrogen bonds defined for protein. 204 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: 0.27 Time building geometry restraints manager: 0.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 552 1.29 - 1.35: 486 1.35 - 1.42: 102 1.42 - 1.48: 504 1.48 - 1.54: 1470 Bond restraints: 3114 Sorted by residual: bond pdb=" CA GLY A 86 " pdb=" C GLY A 86 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 7.88e-01 bond pdb=" CA GLY C 86 " pdb=" C GLY C 86 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 6.69e-01 bond pdb=" CA GLY F 86 " pdb=" C GLY F 86 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 6.38e-01 bond pdb=" CA GLY D 86 " pdb=" C GLY D 86 " ideal model delta sigma weight residual 1.520 1.515 0.006 7.30e-03 1.88e+04 5.82e-01 bond pdb=" CA GLY E 86 " pdb=" C GLY E 86 " ideal model delta sigma weight residual 1.520 1.515 0.005 7.30e-03 1.88e+04 4.87e-01 ... (remaining 3109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.72: 3669 0.72 - 1.43: 415 1.43 - 2.15: 92 2.15 - 2.87: 6 2.87 - 3.58: 12 Bond angle restraints: 4194 Sorted by residual: angle pdb=" N GLY A 86 " pdb=" CA GLY A 86 " pdb=" C GLY A 86 " ideal model delta sigma weight residual 110.71 114.29 -3.58 1.53e+00 4.27e-01 5.48e+00 angle pdb=" N GLY C 86 " pdb=" CA GLY C 86 " pdb=" C GLY C 86 " ideal model delta sigma weight residual 110.71 114.28 -3.57 1.53e+00 4.27e-01 5.44e+00 angle pdb=" N GLY E 86 " pdb=" CA GLY E 86 " pdb=" C GLY E 86 " ideal model delta sigma weight residual 110.71 114.28 -3.57 1.53e+00 4.27e-01 5.44e+00 angle pdb=" N GLY F 86 " pdb=" CA GLY F 86 " pdb=" C GLY F 86 " ideal model delta sigma weight residual 110.71 114.28 -3.57 1.53e+00 4.27e-01 5.43e+00 angle pdb=" N GLY B 86 " pdb=" CA GLY B 86 " pdb=" C GLY B 86 " ideal model delta sigma weight residual 110.71 114.25 -3.54 1.53e+00 4.27e-01 5.37e+00 ... (remaining 4189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 1620 14.55 - 29.11: 174 29.11 - 43.66: 18 43.66 - 58.21: 18 58.21 - 72.76: 6 Dihedral angle restraints: 1836 sinusoidal: 624 harmonic: 1212 Sorted by residual: dihedral pdb=" CA GLY B 41 " pdb=" C GLY B 41 " pdb=" N SER B 42 " pdb=" CA SER B 42 " ideal model delta harmonic sigma weight residual 180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLY C 41 " pdb=" C GLY C 41 " pdb=" N SER C 42 " pdb=" CA SER C 42 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLY F 41 " pdb=" C GLY F 41 " pdb=" N SER F 42 " pdb=" CA SER F 42 " ideal model delta harmonic sigma weight residual -180.00 -160.23 -19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 1833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 251 0.025 - 0.050: 144 0.050 - 0.075: 49 0.075 - 0.099: 29 0.099 - 0.124: 73 Chirality restraints: 546 Sorted by residual: chirality pdb=" CA VAL F 49 " pdb=" N VAL F 49 " pdb=" C VAL F 49 " pdb=" CB VAL F 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA VAL B 49 " pdb=" N VAL B 49 " pdb=" C VAL B 49 " pdb=" CB VAL B 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 543 not shown) Planarity restraints: 522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 43 " -0.004 2.00e-02 2.50e+03 7.94e-03 6.31e-01 pdb=" C LYS C 43 " 0.014 2.00e-02 2.50e+03 pdb=" O LYS C 43 " -0.005 2.00e-02 2.50e+03 pdb=" N THR C 44 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 43 " -0.004 2.00e-02 2.50e+03 7.88e-03 6.21e-01 pdb=" C LYS F 43 " 0.014 2.00e-02 2.50e+03 pdb=" O LYS F 43 " -0.005 2.00e-02 2.50e+03 pdb=" N THR F 44 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 43 " 0.004 2.00e-02 2.50e+03 7.87e-03 6.19e-01 pdb=" C LYS E 43 " -0.014 2.00e-02 2.50e+03 pdb=" O LYS E 43 " 0.005 2.00e-02 2.50e+03 pdb=" N THR E 44 " 0.005 2.00e-02 2.50e+03 ... (remaining 519 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1478 2.98 - 3.46: 2679 3.46 - 3.94: 4531 3.94 - 4.42: 4759 4.42 - 4.90: 9838 Nonbonded interactions: 23285 Sorted by model distance: nonbonded pdb=" O THR F 59 " pdb=" OG1 THR F 59 " model vdw 2.497 3.040 nonbonded pdb=" O THR C 59 " pdb=" OG1 THR C 59 " model vdw 2.497 3.040 nonbonded pdb=" O THR D 59 " pdb=" OG1 THR D 59 " model vdw 2.498 3.040 nonbonded pdb=" O THR A 59 " pdb=" OG1 THR A 59 " model vdw 2.498 3.040 nonbonded pdb=" O THR B 59 " pdb=" OG1 THR B 59 " model vdw 2.498 3.040 ... (remaining 23280 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.400 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.002 0.015 3114 Z= 0.112 Angle : 0.509 3.582 4194 Z= 0.316 Chirality : 0.052 0.124 546 Planarity : 0.002 0.008 522 Dihedral : 13.527 72.763 1068 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.03 (0.27), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.20), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR E 39 PHE 0.006 0.002 PHE A 94 HIS 0.004 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 3114) covalent geometry : angle 0.50946 ( 4194) hydrogen bonds : bond 0.16810 ( 68) hydrogen bonds : angle 8.20649 ( 204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.102 Fit side-chains REVERT: A 94 PHE cc_start: 0.6187 (t80) cc_final: 0.5657 (t80) REVERT: F 94 PHE cc_start: 0.6098 (t80) cc_final: 0.5564 (t80) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0829 time to fit residues: 4.8448 Evaluate side-chains 44 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.0010 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.3608 ------------------------------------------------------------------------------- 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 = 0.4494 r_free = 0.4494 target = 0.187854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.150580 restraints weight = 3246.981| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.65 r_work: 0.3997 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3114 Z= 0.112 Angle : 0.443 4.284 4194 Z= 0.259 Chirality : 0.050 0.127 546 Planarity : 0.002 0.008 522 Dihedral : 4.897 23.002 444 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 1.28 % Allowed : 8.33 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.49 (0.30), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.23), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 39 PHE 0.008 0.002 PHE D 94 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 3114) covalent geometry : angle 0.44286 ( 4194) hydrogen bonds : bond 0.02011 ( 68) hydrogen bonds : angle 5.34974 ( 204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.092 Fit side-chains REVERT: E 46 GLU cc_start: 0.8149 (pt0) cc_final: 0.7768 (pt0) REVERT: E 96 LYS cc_start: 0.6609 (tttt) cc_final: 0.6408 (tttm) REVERT: F 94 PHE cc_start: 0.6330 (t80) cc_final: 0.5591 (t80) REVERT: C 94 PHE cc_start: 0.5757 (t80) cc_final: 0.4788 (t80) outliers start: 4 outliers final: 2 residues processed: 43 average time/residue: 0.0856 time to fit residues: 4.2083 Evaluate side-chains 44 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain F residue 43 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4385 r_free = 0.4385 target = 0.178071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.139478 restraints weight = 3307.112| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.66 r_work: 0.3850 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 3114 Z= 0.297 Angle : 0.587 3.822 4194 Z= 0.344 Chirality : 0.054 0.127 546 Planarity : 0.002 0.009 522 Dihedral : 5.710 26.615 444 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.08 % Favored : 85.92 % Rotamer: Outliers : 2.88 % Allowed : 11.54 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.39 (0.30), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.23), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR E 39 PHE 0.010 0.002 PHE F 94 HIS 0.007 0.004 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00686 ( 3114) covalent geometry : angle 0.58679 ( 4194) hydrogen bonds : bond 0.02576 ( 68) hydrogen bonds : angle 5.50252 ( 204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.068 Fit side-chains REVERT: A 94 PHE cc_start: 0.6510 (t80) cc_final: 0.5578 (t80) REVERT: D 96 LYS cc_start: 0.7373 (tttt) cc_final: 0.7134 (tttm) REVERT: F 94 PHE cc_start: 0.6310 (t80) cc_final: 0.5601 (t80) REVERT: B 96 LYS cc_start: 0.7360 (tttt) cc_final: 0.7106 (tttp) REVERT: C 94 PHE cc_start: 0.5724 (t80) cc_final: 0.4560 (t80) outliers start: 9 outliers final: 8 residues processed: 54 average time/residue: 0.0691 time to fit residues: 4.3294 Evaluate side-chains 56 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 99 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.0470 overall best weight: 1.6084 ------------------------------------------------------------------------------- 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 = 0.4479 r_free = 0.4479 target = 0.185651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.148268 restraints weight = 3193.622| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.61 r_work: 0.4010 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3114 Z= 0.125 Angle : 0.434 3.702 4194 Z= 0.255 Chirality : 0.050 0.127 546 Planarity : 0.002 0.008 522 Dihedral : 4.937 23.705 444 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 2.88 % Allowed : 13.14 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.97 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 39 PHE 0.009 0.002 PHE F 94 HIS 0.004 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3114) covalent geometry : angle 0.43380 ( 4194) hydrogen bonds : bond 0.01530 ( 68) hydrogen bonds : angle 4.82739 ( 204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.134 Fit side-chains REVERT: A 94 PHE cc_start: 0.6351 (t80) cc_final: 0.5460 (t80) REVERT: F 94 PHE cc_start: 0.6165 (t80) cc_final: 0.5298 (t80) outliers start: 9 outliers final: 8 residues processed: 50 average time/residue: 0.0655 time to fit residues: 3.8960 Evaluate side-chains 50 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- 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 = 0.4517 r_free = 0.4517 target = 0.189472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.151819 restraints weight = 3188.122| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.63 r_work: 0.4017 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3114 Z= 0.108 Angle : 0.405 3.646 4194 Z= 0.238 Chirality : 0.050 0.125 546 Planarity : 0.002 0.008 522 Dihedral : 4.564 21.514 444 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 3.21 % Allowed : 13.14 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.73 (0.35), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 39 PHE 0.007 0.002 PHE F 94 HIS 0.004 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 3114) covalent geometry : angle 0.40535 ( 4194) hydrogen bonds : bond 0.01293 ( 68) hydrogen bonds : angle 4.47262 ( 204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.093 Fit side-chains REVERT: E 94 PHE cc_start: 0.5421 (t80) cc_final: 0.4406 (t80) REVERT: F 94 PHE cc_start: 0.6122 (t80) cc_final: 0.5282 (t80) REVERT: C 94 PHE cc_start: 0.5303 (t80) cc_final: 0.4073 (t80) outliers start: 10 outliers final: 9 residues processed: 47 average time/residue: 0.0777 time to fit residues: 4.2722 Evaluate side-chains 48 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.4475 r_free = 0.4475 target = 0.185939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.148061 restraints weight = 3187.712| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 2.55 r_work: 0.4003 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3114 Z= 0.161 Angle : 0.445 3.721 4194 Z= 0.263 Chirality : 0.050 0.127 546 Planarity : 0.002 0.009 522 Dihedral : 4.877 22.887 444 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 3.21 % Allowed : 13.14 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.67 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR F 39 PHE 0.009 0.002 PHE F 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 3114) covalent geometry : angle 0.44530 ( 4194) hydrogen bonds : bond 0.01496 ( 68) hydrogen bonds : angle 4.58627 ( 204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.112 Fit side-chains REVERT: E 94 PHE cc_start: 0.5552 (t80) cc_final: 0.4558 (t80) REVERT: F 94 PHE cc_start: 0.6167 (t80) cc_final: 0.5342 (t80) REVERT: C 94 PHE cc_start: 0.5378 (t80) cc_final: 0.4143 (t80) outliers start: 10 outliers final: 9 residues processed: 47 average time/residue: 0.0694 time to fit residues: 3.9642 Evaluate side-chains 48 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4496 r_free = 0.4496 target = 0.187640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.149884 restraints weight = 3231.878| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.56 r_work: 0.3994 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3114 Z= 0.132 Angle : 0.420 3.670 4194 Z= 0.247 Chirality : 0.050 0.126 546 Planarity : 0.002 0.009 522 Dihedral : 4.705 22.023 444 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.21 % Allowed : 13.78 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.55 (0.35), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR F 39 PHE 0.009 0.002 PHE F 94 HIS 0.005 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3114) covalent geometry : angle 0.42003 ( 4194) hydrogen bonds : bond 0.01308 ( 68) hydrogen bonds : angle 4.39188 ( 204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.106 Fit side-chains REVERT: E 94 PHE cc_start: 0.5290 (t80) cc_final: 0.4208 (t80) REVERT: F 94 PHE cc_start: 0.6276 (t80) cc_final: 0.5354 (t80) REVERT: C 94 PHE cc_start: 0.5393 (t80) cc_final: 0.4065 (t80) outliers start: 10 outliers final: 10 residues processed: 46 average time/residue: 0.0690 time to fit residues: 3.8671 Evaluate side-chains 48 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.4446 r_free = 0.4446 target = 0.183246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.145322 restraints weight = 3285.273| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.56 r_work: 0.3980 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3114 Z= 0.200 Angle : 0.476 3.860 4194 Z= 0.280 Chirality : 0.051 0.127 546 Planarity : 0.002 0.009 522 Dihedral : 5.059 23.609 444 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 3.85 % Allowed : 12.82 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.60 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR F 39 PHE 0.010 0.002 PHE A 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 3114) covalent geometry : angle 0.47601 ( 4194) hydrogen bonds : bond 0.01630 ( 68) hydrogen bonds : angle 4.61302 ( 204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.116 Fit side-chains REVERT: A 94 PHE cc_start: 0.6268 (t80) cc_final: 0.5431 (t80) REVERT: E 94 PHE cc_start: 0.5304 (t80) cc_final: 0.4164 (t80) REVERT: F 94 PHE cc_start: 0.6182 (t80) cc_final: 0.5300 (t80) REVERT: C 94 PHE cc_start: 0.5320 (t80) cc_final: 0.4093 (t80) outliers start: 12 outliers final: 12 residues processed: 50 average time/residue: 0.0595 time to fit residues: 3.6242 Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 0.0370 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.1862 ------------------------------------------------------------------------------- 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 = 0.4473 r_free = 0.4473 target = 0.186215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.148681 restraints weight = 3241.595| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.58 r_work: 0.4000 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3114 Z= 0.162 Angle : 0.445 3.650 4194 Z= 0.262 Chirality : 0.050 0.127 546 Planarity : 0.002 0.009 522 Dihedral : 4.904 22.891 444 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 4.17 % Allowed : 12.82 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.51 (0.35), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR F 39 PHE 0.009 0.002 PHE A 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3114) covalent geometry : angle 0.44506 ( 4194) hydrogen bonds : bond 0.01443 ( 68) hydrogen bonds : angle 4.48125 ( 204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.101 Fit side-chains REVERT: A 94 PHE cc_start: 0.6277 (t80) cc_final: 0.5461 (t80) REVERT: E 94 PHE cc_start: 0.5259 (t80) cc_final: 0.4131 (t80) REVERT: F 94 PHE cc_start: 0.6153 (t80) cc_final: 0.5292 (t80) REVERT: C 94 PHE cc_start: 0.5387 (t80) cc_final: 0.4142 (t80) outliers start: 13 outliers final: 12 residues processed: 51 average time/residue: 0.0696 time to fit residues: 4.2938 Evaluate side-chains 53 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.2980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.4500 r_free = 0.4500 target = 0.188875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.151421 restraints weight = 3183.847| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.55 r_work: 0.4025 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3114 Z= 0.137 Angle : 0.422 3.755 4194 Z= 0.249 Chirality : 0.050 0.126 546 Planarity : 0.002 0.009 522 Dihedral : 4.698 21.985 444 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 3.85 % Allowed : 13.78 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.44 (0.35), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 39 PHE 0.009 0.002 PHE F 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3114) covalent geometry : angle 0.42189 ( 4194) hydrogen bonds : bond 0.01320 ( 68) hydrogen bonds : angle 4.36189 ( 204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.117 Fit side-chains REVERT: A 94 PHE cc_start: 0.6235 (t80) cc_final: 0.5411 (t80) REVERT: E 94 PHE cc_start: 0.5081 (t80) cc_final: 0.3925 (t80) REVERT: F 94 PHE cc_start: 0.6118 (t80) cc_final: 0.5251 (t80) REVERT: C 94 PHE cc_start: 0.5100 (t80) cc_final: 0.3845 (t80) outliers start: 12 outliers final: 12 residues processed: 49 average time/residue: 0.0610 time to fit residues: 3.7524 Evaluate side-chains 51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.4448 r_free = 0.4448 target = 0.183736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.145879 restraints weight = 3284.309| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.64 r_work: 0.3964 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3114 Z= 0.202 Angle : 0.480 3.792 4194 Z= 0.283 Chirality : 0.051 0.127 546 Planarity : 0.002 0.009 522 Dihedral : 5.050 23.522 444 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 4.49 % Allowed : 13.46 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.54 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR F 39 PHE 0.010 0.002 PHE A 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 3114) covalent geometry : angle 0.47970 ( 4194) hydrogen bonds : bond 0.01629 ( 68) hydrogen bonds : angle 4.58330 ( 204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 855.76 seconds wall clock time: 15 minutes 20.55 seconds (920.55 seconds total)