Starting phenix.real_space_refine on Fri Dec 27 06:07:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hzc_35088/12_2024/8hzc_35088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hzc_35088/12_2024/8hzc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hzc_35088/12_2024/8hzc_35088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hzc_35088/12_2024/8hzc_35088.map" model { file = "/net/cci-nas-00/data/ceres_data/8hzc_35088/12_2024/8hzc_35088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hzc_35088/12_2024/8hzc_35088.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: C, B, E, D, F Time building chain proxies: 2.20, per 1000 atoms: 0.71 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: 0.74 Conformation dependent library (CDL) restraints added in 458.2 milliseconds 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: 0.45 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: 0.70 Time building geometry restraints manager: 0.86 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.570 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.280 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.210 ------------------------------------------------------------------------------- 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= 0.139 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.004 0.002 HIS C 50 PHE 0.006 0.002 PHE A 94 TYR 0.004 0.001 TYR E 39 *********************** 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 : 0.345 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: 0.2412 time to fit residues: 14.1238 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 : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.0270 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3114 Z= 0.265 Angle : 0.488 4.338 4194 Z= 0.286 Chirality : 0.051 0.127 546 Planarity : 0.002 0.008 522 Dihedral : 5.263 24.781 444 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 1.60 % Allowed : 9.29 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.29), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.22), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.008 0.002 PHE D 94 TYR 0.009 0.002 TYR B 39 *********************** 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: 5 poor density : 42 time to evaluate : 0.348 Fit side-chains REVERT: F 94 PHE cc_start: 0.6075 (t80) cc_final: 0.5628 (t80) REVERT: C 94 PHE cc_start: 0.5602 (t80) cc_final: 0.4827 (t80) outliers start: 5 outliers final: 4 residues processed: 43 average time/residue: 0.2322 time to fit residues: 11.5315 Evaluate side-chains 45 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 0.1980 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3114 Z= 0.297 Angle : 0.492 3.791 4194 Z= 0.289 Chirality : 0.051 0.125 546 Planarity : 0.002 0.008 522 Dihedral : 5.244 24.026 444 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 3.21 % Allowed : 11.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.008 0.002 PHE A 94 TYR 0.008 0.002 TYR B 39 *********************** 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 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.341 Fit side-chains REVERT: A 94 PHE cc_start: 0.6068 (t80) cc_final: 0.5327 (t80) REVERT: F 94 PHE cc_start: 0.5881 (t80) cc_final: 0.5355 (t80) REVERT: C 94 PHE cc_start: 0.5275 (t80) cc_final: 0.4273 (t80) outliers start: 10 outliers final: 8 residues processed: 51 average time/residue: 0.2108 time to fit residues: 12.5662 Evaluate side-chains 51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 79 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3114 Z= 0.268 Angle : 0.467 4.083 4194 Z= 0.275 Chirality : 0.051 0.126 546 Planarity : 0.002 0.009 522 Dihedral : 5.086 23.654 444 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 3.53 % Allowed : 12.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.009 0.002 PHE F 94 TYR 0.008 0.002 TYR E 39 *********************** 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 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.370 Fit side-chains REVERT: A 94 PHE cc_start: 0.6070 (t80) cc_final: 0.5274 (t80) REVERT: F 94 PHE cc_start: 0.5924 (t80) cc_final: 0.5177 (t80) outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 0.2032 time to fit residues: 12.0732 Evaluate side-chains 51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 3114 Z= 0.526 Angle : 0.609 3.614 4194 Z= 0.358 Chirality : 0.055 0.126 546 Planarity : 0.003 0.010 522 Dihedral : 5.847 27.232 444 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.91 % Favored : 87.09 % Rotamer: Outliers : 4.49 % Allowed : 12.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS A 50 PHE 0.010 0.002 PHE F 94 TYR 0.011 0.003 TYR B 39 *********************** 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 61 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.373 Fit side-chains REVERT: A 94 PHE cc_start: 0.6137 (t80) cc_final: 0.5471 (t80) REVERT: E 94 PHE cc_start: 0.5440 (t80) cc_final: 0.4392 (t80) REVERT: F 94 PHE cc_start: 0.6005 (t80) cc_final: 0.5354 (t80) REVERT: C 94 PHE cc_start: 0.5314 (t80) cc_final: 0.4175 (t80) REVERT: C 99 GLN cc_start: 0.6868 (OUTLIER) cc_final: 0.6659 (mm-40) outliers start: 14 outliers final: 13 residues processed: 57 average time/residue: 0.1919 time to fit residues: 13.0389 Evaluate side-chains 61 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 15 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 Chi-restraints excluded: chain C residue 99 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3114 Z= 0.293 Angle : 0.485 3.954 4194 Z= 0.285 Chirality : 0.051 0.129 546 Planarity : 0.002 0.009 522 Dihedral : 5.293 24.905 444 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 4.49 % Allowed : 12.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.010 0.002 PHE F 94 TYR 0.008 0.002 TYR B 39 *********************** 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 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.349 Fit side-chains REVERT: A 94 PHE cc_start: 0.6086 (t80) cc_final: 0.5393 (t80) REVERT: E 94 PHE cc_start: 0.5385 (t80) cc_final: 0.4358 (t80) REVERT: F 43 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7741 (ptmt) REVERT: F 94 PHE cc_start: 0.5965 (t80) cc_final: 0.5298 (t80) REVERT: C 94 PHE cc_start: 0.5282 (t80) cc_final: 0.4160 (t80) outliers start: 14 outliers final: 10 residues processed: 53 average time/residue: 0.1867 time to fit residues: 11.7579 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 : 0.003 0.017 3114 Z= 0.211 Angle : 0.432 3.702 4194 Z= 0.254 Chirality : 0.050 0.128 546 Planarity : 0.002 0.009 522 Dihedral : 4.895 22.941 444 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 3.53 % Allowed : 14.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.009 0.002 PHE F 94 TYR 0.006 0.002 TYR B 39 *********************** 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 51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.306 Fit side-chains REVERT: A 94 PHE cc_start: 0.6002 (t80) cc_final: 0.5285 (t80) REVERT: E 94 PHE cc_start: 0.5101 (t80) cc_final: 0.4057 (t80) REVERT: F 94 PHE cc_start: 0.5898 (t80) cc_final: 0.5177 (t80) REVERT: C 94 PHE cc_start: 0.5191 (t80) cc_final: 0.4013 (t80) outliers start: 11 outliers final: 10 residues processed: 49 average time/residue: 0.1593 time to fit residues: 9.4683 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 : 0.375 ------------------------------------------------------------------------------- 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 75 THR Chi-restraints excluded: chain F residue 37 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 0.0170 chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 3114 Z= 0.137 Angle : 0.389 3.669 4194 Z= 0.229 Chirality : 0.049 0.126 546 Planarity : 0.002 0.009 522 Dihedral : 4.472 21.250 444 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 2.88 % Allowed : 15.71 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.36), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.007 0.002 PHE F 94 TYR 0.005 0.001 TYR B 39 *********************** 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 47 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.319 Fit side-chains REVERT: E 94 PHE cc_start: 0.4825 (t80) cc_final: 0.3855 (t80) REVERT: F 94 PHE cc_start: 0.5761 (t80) cc_final: 0.5046 (t80) REVERT: C 94 PHE cc_start: 0.5119 (t80) cc_final: 0.3869 (t80) outliers start: 9 outliers final: 8 residues processed: 45 average time/residue: 0.1480 time to fit residues: 8.3267 Evaluate side-chains 47 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 F residue 37 VAL Chi-restraints excluded: chain B residue 37 VAL 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 35 optimal weight: 7.9990 chunk 37 optimal weight: 0.0870 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2063 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= 0.156 Angle : 0.394 3.727 4194 Z= 0.233 Chirality : 0.049 0.125 546 Planarity : 0.002 0.009 522 Dihedral : 4.442 21.141 444 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.53 % Allowed : 15.71 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.36), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.008 0.002 PHE F 94 TYR 0.006 0.001 TYR B 39 *********************** 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 49 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.317 Fit side-chains REVERT: E 94 PHE cc_start: 0.4806 (t80) cc_final: 0.3799 (t80) REVERT: F 94 PHE cc_start: 0.5729 (t80) cc_final: 0.4981 (t80) REVERT: C 94 PHE cc_start: 0.4980 (t80) cc_final: 0.3691 (t80) outliers start: 11 outliers final: 10 residues processed: 48 average time/residue: 0.1357 time to fit residues: 8.2207 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 : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 75 THR 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 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 20 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.0470 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2128 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= 0.150 Angle : 0.389 3.632 4194 Z= 0.230 Chirality : 0.049 0.125 546 Planarity : 0.002 0.009 522 Dihedral : 4.374 20.864 444 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 3.53 % Allowed : 15.38 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.008 0.002 PHE F 94 TYR 0.006 0.001 TYR F 39 ********************** 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 48 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.324 Fit side-chains REVERT: E 94 PHE cc_start: 0.4834 (t80) cc_final: 0.3796 (t80) REVERT: F 94 PHE cc_start: 0.5780 (t80) cc_final: 0.5010 (t80) REVERT: C 94 PHE cc_start: 0.4866 (t80) cc_final: 0.3566 (t80) outliers start: 11 outliers final: 11 residues processed: 48 average time/residue: 0.1341 time to fit residues: 8.1277 Evaluate side-chains 48 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL 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 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: 0.2980 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.4523 r_free = 0.4523 target = 0.190632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.153269 restraints weight = 3210.450| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.51 r_work: 0.4057 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3114 Z= 0.187 Angle : 0.406 3.637 4194 Z= 0.240 Chirality : 0.049 0.125 546 Planarity : 0.002 0.009 522 Dihedral : 4.488 21.133 444 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 3.53 % Allowed : 15.38 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.008 0.002 PHE F 94 TYR 0.007 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1203.03 seconds wall clock time: 22 minutes 50.77 seconds (1370.77 seconds total)