Starting phenix.real_space_refine on Mon Sep 23 13:13:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzb_35087/09_2024/8hzb_35087.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzb_35087/09_2024/8hzb_35087.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzb_35087/09_2024/8hzb_35087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzb_35087/09_2024/8hzb_35087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzb_35087/09_2024/8hzb_35087.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzb_35087/09_2024/8hzb_35087.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= 0.002 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 1860 2.51 5 N 516 2.21 5 O 600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2976 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 496 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.93, per 1000 atoms: 0.65 Number of scatterers: 2976 At special positions: 0 Unit cell: (96.28, 121.18, 36.52, 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 600 8.00 N 516 7.00 C 1860 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 471.2 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 50.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 15 through 21 removed outlier: 6.545A pdb=" N VAL D 16 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ALA E 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA D 18 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS E 21 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU D 20 " --> pdb=" O LYS E 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 58 removed outlier: 6.799A pdb=" N GLY C 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL D 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA C 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR D 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA D 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU C 57 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL D 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL E 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N HIS D 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY E 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 62 through 66 removed outlier: 6.526A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 69 through 80 removed outlier: 9.129A pdb=" N VAL D 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 10.489A pdb=" N GLY C 73 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR D 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N THR C 75 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL D 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL C 77 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ALA D 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N GLN C 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ALA D 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL E 70 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL D 71 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR E 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY D 73 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL D 77 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA E 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN D 79 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS E 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.784A pdb=" N PHE C 94 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N THR D 92 " --> pdb=" O GLY E 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 97 through 98 removed outlier: 6.906A pdb=" N LYS D 97 " --> pdb=" O ASP E 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 15 through 21 removed outlier: 6.526A pdb=" N VAL F 16 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N ALA B 19 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA F 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N LYS B 21 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU F 20 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 46 through 58 removed outlier: 6.821A pdb=" N GLY A 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL F 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA A 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR F 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 55 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA F 56 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU A 57 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL F 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS F 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY B 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 62 through 66 removed outlier: 6.572A pdb=" N VAL F 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL B 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN F 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 69 through 80 removed outlier: 9.115A pdb=" N VAL F 70 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N GLY A 73 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR F 72 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR A 75 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL F 74 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL A 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA F 76 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N GLN A 79 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N ALA F 78 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B 70 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL F 71 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR B 72 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY F 73 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL F 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA B 78 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLN F 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS B 80 " --> pdb=" O GLN F 79 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.805A pdb=" N PHE A 94 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N THR F 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 97 through 98 removed outlier: 6.896A pdb=" N LYS F 97 " --> pdb=" O ASP B 98 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 162 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: 0.65 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: 1.22 - 1.29: 528 1.29 - 1.35: 460 1.35 - 1.42: 102 1.42 - 1.48: 501 1.48 - 1.55: 1391 Bond restraints: 2982 Sorted by residual: bond pdb=" CA LYS A 58 " pdb=" C LYS A 58 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.08e-02 8.57e+03 2.16e+00 bond pdb=" CA LYS E 58 " pdb=" C LYS E 58 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.08e-02 8.57e+03 2.07e+00 bond pdb=" CA LYS C 58 " pdb=" C LYS C 58 " ideal model delta sigma weight residual 1.526 1.511 0.015 1.08e-02 8.57e+03 1.95e+00 bond pdb=" CA LYS B 58 " pdb=" C LYS B 58 " ideal model delta sigma weight residual 1.526 1.511 0.015 1.08e-02 8.57e+03 1.94e+00 bond pdb=" CA LYS D 58 " pdb=" C LYS D 58 " ideal model delta sigma weight residual 1.526 1.511 0.015 1.08e-02 8.57e+03 1.92e+00 ... (remaining 2977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 3486 1.14 - 2.28: 412 2.28 - 3.42: 93 3.42 - 4.56: 23 4.56 - 5.70: 12 Bond angle restraints: 4026 Sorted by residual: angle pdb=" C GLY E 41 " pdb=" N SER E 42 " pdb=" CA SER E 42 " ideal model delta sigma weight residual 122.42 117.96 4.46 1.55e+00 4.16e-01 8.26e+00 angle pdb=" C GLY A 41 " pdb=" N SER A 42 " pdb=" CA SER A 42 " ideal model delta sigma weight residual 122.42 117.97 4.45 1.55e+00 4.16e-01 8.24e+00 angle pdb=" C GLY B 41 " pdb=" N SER B 42 " pdb=" CA SER B 42 " ideal model delta sigma weight residual 122.42 117.97 4.45 1.55e+00 4.16e-01 8.23e+00 angle pdb=" C GLY D 41 " pdb=" N SER D 42 " pdb=" CA SER D 42 " ideal model delta sigma weight residual 122.42 117.97 4.45 1.55e+00 4.16e-01 8.23e+00 angle pdb=" C GLY C 41 " pdb=" N SER C 42 " pdb=" CA SER C 42 " ideal model delta sigma weight residual 122.42 118.01 4.41 1.55e+00 4.16e-01 8.11e+00 ... (remaining 4021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 1524 17.62 - 35.24: 186 35.24 - 52.85: 30 52.85 - 70.47: 0 70.47 - 88.09: 12 Dihedral angle restraints: 1752 sinusoidal: 582 harmonic: 1170 Sorted by residual: dihedral pdb=" CA VAL A 40 " pdb=" C VAL A 40 " pdb=" N GLY A 41 " pdb=" CA GLY A 41 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA VAL D 40 " pdb=" C VAL D 40 " pdb=" N GLY D 41 " pdb=" CA GLY D 41 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA VAL F 40 " pdb=" C VAL F 40 " pdb=" N GLY F 41 " pdb=" CA GLY F 41 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 1749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 148 0.026 - 0.051: 160 0.051 - 0.077: 99 0.077 - 0.102: 71 0.102 - 0.128: 56 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 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 3.90e-01 chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 531 not shown) Planarity restraints: 498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 66 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C VAL C 66 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL C 66 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY C 67 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 66 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.86e+00 pdb=" C VAL E 66 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL E 66 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY E 67 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 66 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C VAL B 66 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL B 66 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY B 67 " -0.008 2.00e-02 2.50e+03 ... (remaining 495 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 154 2.71 - 3.26: 2853 3.26 - 3.80: 4388 3.80 - 4.35: 5053 4.35 - 4.90: 10336 Nonbonded interactions: 22784 Sorted by model distance: nonbonded pdb=" OE2 GLU F 46 " pdb=" NZ LYS F 80 " model vdw 2.162 3.120 nonbonded pdb=" OE2 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.162 3.120 nonbonded pdb=" OE2 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.162 3.120 nonbonded pdb=" OE2 GLU B 46 " pdb=" NZ LYS B 80 " model vdw 2.162 3.120 nonbonded pdb=" OE2 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.162 3.120 ... (remaining 22779 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: 1.830 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.620 Find NCS groups from input model: 0.100 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 : 0.008 0.044 2982 Z= 0.575 Angle : 0.920 5.699 4026 Z= 0.518 Chirality : 0.059 0.128 534 Planarity : 0.004 0.014 498 Dihedral : 16.623 88.088 1008 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % 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: -4.16 (0.28), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.22), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.019 0.006 PHE C 94 TYR 0.019 0.005 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.304 Fit side-chains REVERT: C 45 LYS cc_start: 0.7387 (tttt) cc_final: 0.7140 (tttm) REVERT: E 45 LYS cc_start: 0.7543 (tttt) cc_final: 0.7095 (tttm) REVERT: F 45 LYS cc_start: 0.7570 (tttt) cc_final: 0.7092 (tttm) REVERT: A 45 LYS cc_start: 0.7425 (tttt) cc_final: 0.7175 (tttm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1890 time to fit residues: 5.3883 Evaluate side-chains 23 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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: 0.0470 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- 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: 0.6871 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2982 Z= 0.151 Angle : 0.570 4.699 4026 Z= 0.309 Chirality : 0.051 0.133 534 Planarity : 0.002 0.012 498 Dihedral : 5.979 21.996 426 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.00 % Allowed : 24.67 % Favored : 73.33 % 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: -3.37 (0.35), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 50 PHE 0.006 0.002 PHE B 94 TYR 0.007 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 17 time to evaluate : 0.307 Fit side-chains REVERT: E 45 LYS cc_start: 0.7628 (tttt) cc_final: 0.7118 (tttm) REVERT: B 45 LYS cc_start: 0.7532 (tttt) cc_final: 0.7080 (tttm) outliers start: 6 outliers final: 6 residues processed: 23 average time/residue: 0.1106 time to fit residues: 3.5824 Evaluate side-chains 23 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 17 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 0.0980 chunk 37 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN C 65 ASN F 65 ASN A 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2982 Z= 0.240 Angle : 0.635 5.287 4026 Z= 0.340 Chirality : 0.052 0.130 534 Planarity : 0.002 0.013 498 Dihedral : 6.241 20.925 426 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 4.67 % Allowed : 23.00 % Favored : 72.33 % 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: -3.15 (0.37), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS D 50 PHE 0.009 0.003 PHE B 94 TYR 0.013 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 20 time to evaluate : 0.320 Fit side-chains REVERT: C 44 THR cc_start: 0.6766 (OUTLIER) cc_final: 0.6522 (t) REVERT: E 44 THR cc_start: 0.6863 (OUTLIER) cc_final: 0.6604 (t) REVERT: E 45 LYS cc_start: 0.7688 (tttt) cc_final: 0.7201 (tttm) REVERT: F 44 THR cc_start: 0.6863 (OUTLIER) cc_final: 0.6535 (t) REVERT: A 44 THR cc_start: 0.6899 (OUTLIER) cc_final: 0.6598 (t) REVERT: B 44 THR cc_start: 0.6746 (OUTLIER) cc_final: 0.6529 (t) REVERT: B 45 LYS cc_start: 0.7611 (tttt) cc_final: 0.7218 (tttm) outliers start: 14 outliers final: 8 residues processed: 32 average time/residue: 0.0961 time to fit residues: 4.3851 Evaluate side-chains 33 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 20 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.0670 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 overall best weight: 3.0126 ------------------------------------------------------------------------------- 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: 0.7034 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2982 Z= 0.346 Angle : 0.733 6.584 4026 Z= 0.392 Chirality : 0.053 0.128 534 Planarity : 0.003 0.014 498 Dihedral : 6.832 21.296 426 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 9.00 % Allowed : 22.33 % Favored : 68.67 % 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: -3.21 (0.36), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS D 50 PHE 0.014 0.004 PHE E 94 TYR 0.015 0.004 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 23 time to evaluate : 0.284 Fit side-chains REVERT: E 44 THR cc_start: 0.6872 (OUTLIER) cc_final: 0.6557 (t) REVERT: E 45 LYS cc_start: 0.7746 (tttt) cc_final: 0.7271 (tttm) REVERT: F 44 THR cc_start: 0.6950 (OUTLIER) cc_final: 0.6621 (t) REVERT: A 44 THR cc_start: 0.6819 (OUTLIER) cc_final: 0.6584 (p) REVERT: B 44 THR cc_start: 0.6893 (OUTLIER) cc_final: 0.6652 (t) REVERT: B 45 LYS cc_start: 0.7697 (tttt) cc_final: 0.7317 (tttm) outliers start: 27 outliers final: 17 residues processed: 44 average time/residue: 0.0937 time to fit residues: 5.7025 Evaluate side-chains 44 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 23 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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: 0.6942 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2982 Z= 0.170 Angle : 0.579 5.170 4026 Z= 0.309 Chirality : 0.051 0.129 534 Planarity : 0.002 0.012 498 Dihedral : 5.883 19.835 426 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 7.33 % Allowed : 24.00 % Favored : 68.67 % 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: -3.06 (0.37), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 50 PHE 0.007 0.002 PHE B 94 TYR 0.007 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 17 time to evaluate : 0.288 Fit side-chains REVERT: E 44 THR cc_start: 0.6758 (OUTLIER) cc_final: 0.6506 (t) REVERT: E 45 LYS cc_start: 0.7759 (tttt) cc_final: 0.7280 (tttm) REVERT: F 44 THR cc_start: 0.6642 (OUTLIER) cc_final: 0.6387 (t) REVERT: B 45 LYS cc_start: 0.7706 (tttt) cc_final: 0.7257 (tttm) outliers start: 22 outliers final: 14 residues processed: 38 average time/residue: 0.1070 time to fit residues: 5.4320 Evaluate side-chains 31 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 15 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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: 0.7039 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2982 Z= 0.334 Angle : 0.708 6.563 4026 Z= 0.377 Chirality : 0.053 0.128 534 Planarity : 0.003 0.014 498 Dihedral : 6.694 19.760 426 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 6.67 % Allowed : 24.00 % Favored : 69.33 % 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: -3.07 (0.36), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS F 50 PHE 0.013 0.004 PHE B 94 TYR 0.014 0.004 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 21 time to evaluate : 0.313 Fit side-chains REVERT: E 44 THR cc_start: 0.6831 (OUTLIER) cc_final: 0.6503 (t) REVERT: E 45 LYS cc_start: 0.7771 (tttt) cc_final: 0.7319 (tttm) REVERT: F 44 THR cc_start: 0.6989 (OUTLIER) cc_final: 0.6766 (t) REVERT: B 45 LYS cc_start: 0.7826 (tttt) cc_final: 0.7392 (tttm) outliers start: 20 outliers final: 15 residues processed: 38 average time/residue: 0.0997 time to fit residues: 5.1729 Evaluate side-chains 38 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 21 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.6945 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2982 Z= 0.172 Angle : 0.572 5.129 4026 Z= 0.306 Chirality : 0.050 0.129 534 Planarity : 0.002 0.013 498 Dihedral : 5.816 19.350 426 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 5.00 % Allowed : 24.67 % Favored : 70.33 % 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: -2.96 (0.37), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 50 PHE 0.007 0.002 PHE B 94 TYR 0.007 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 15 time to evaluate : 0.237 Fit side-chains REVERT: F 44 THR cc_start: 0.6760 (OUTLIER) cc_final: 0.6484 (t) outliers start: 15 outliers final: 13 residues processed: 28 average time/residue: 0.0634 time to fit residues: 2.8756 Evaluate side-chains 29 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 15 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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: 0.6951 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2982 Z= 0.179 Angle : 0.567 4.903 4026 Z= 0.303 Chirality : 0.050 0.128 534 Planarity : 0.002 0.013 498 Dihedral : 5.690 18.430 426 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 4.33 % Allowed : 25.00 % Favored : 70.67 % 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: -2.86 (0.38), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 50 PHE 0.007 0.002 PHE B 94 TYR 0.009 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 15 time to evaluate : 0.326 Fit side-chains REVERT: E 45 LYS cc_start: 0.7653 (tttt) cc_final: 0.7174 (tttm) REVERT: F 44 THR cc_start: 0.6704 (OUTLIER) cc_final: 0.6456 (t) outliers start: 13 outliers final: 12 residues processed: 26 average time/residue: 0.1103 time to fit residues: 4.0830 Evaluate side-chains 27 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 14 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 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: 0.7030 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2982 Z= 0.293 Angle : 0.680 6.432 4026 Z= 0.361 Chirality : 0.052 0.127 534 Planarity : 0.003 0.014 498 Dihedral : 6.545 19.112 426 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 5.67 % Allowed : 23.67 % Favored : 70.67 % 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: -2.90 (0.37), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS D 50 PHE 0.012 0.004 PHE B 94 TYR 0.011 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 19 time to evaluate : 0.301 Fit side-chains REVERT: E 45 LYS cc_start: 0.7714 (tttt) cc_final: 0.7253 (tttm) REVERT: F 44 THR cc_start: 0.6786 (OUTLIER) cc_final: 0.6515 (t) REVERT: B 45 LYS cc_start: 0.7796 (tttt) cc_final: 0.7377 (tttm) outliers start: 17 outliers final: 15 residues processed: 33 average time/residue: 0.1076 time to fit residues: 4.8163 Evaluate side-chains 36 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 20 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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: 0.6987 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2982 Z= 0.217 Angle : 0.601 5.501 4026 Z= 0.321 Chirality : 0.051 0.130 534 Planarity : 0.002 0.013 498 Dihedral : 6.018 17.671 426 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 5.33 % Allowed : 24.33 % Favored : 70.33 % 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: -2.86 (0.38), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 50 PHE 0.008 0.002 PHE B 94 TYR 0.009 0.002 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 20 time to evaluate : 0.294 Fit side-chains REVERT: E 45 LYS cc_start: 0.7665 (tttt) cc_final: 0.7217 (tttm) REVERT: F 44 THR cc_start: 0.6681 (OUTLIER) cc_final: 0.6462 (t) REVERT: B 45 LYS cc_start: 0.7808 (tttt) cc_final: 0.7377 (tttm) outliers start: 16 outliers final: 15 residues processed: 33 average time/residue: 0.1103 time to fit residues: 4.8845 Evaluate side-chains 36 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 20 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.5064 r_free = 0.5064 target = 0.255569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.220583 restraints weight = 3322.136| |-----------------------------------------------------------------------------| r_work (start): 0.4709 rms_B_bonded: 2.76 r_work: 0.4629 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2982 Z= 0.152 Angle : 0.542 4.542 4026 Z= 0.291 Chirality : 0.050 0.128 534 Planarity : 0.002 0.013 498 Dihedral : 5.553 16.877 426 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 4.00 % Allowed : 25.67 % Favored : 70.33 % 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: -2.74 (0.38), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 50 PHE 0.005 0.001 PHE B 94 TYR 0.006 0.001 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1078.91 seconds wall clock time: 19 minutes 47.14 seconds (1187.14 seconds total)