Starting phenix.real_space_refine on Thu Nov 14 05:06:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zlp_60232/11_2024/8zlp_60232.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zlp_60232/11_2024/8zlp_60232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zlp_60232/11_2024/8zlp_60232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zlp_60232/11_2024/8zlp_60232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zlp_60232/11_2024/8zlp_60232.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zlp_60232/11_2024/8zlp_60232.cif" } resolution = 3.5 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= 0.003 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2574 2.51 5 N 708 2.21 5 O 822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4116 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 686 Unusual residues: {'ACE': 1} Classifications: {'peptide': 98, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 97} Restraints were copied for chains: C, B, G, F, H Time building chain proxies: 2.68, per 1000 atoms: 0.65 Number of scatterers: 4116 At special positions: 0 Unit cell: (135.29, 118.69, 32.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 822 8.00 N 708 7.00 C 2574 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: 0.99 Conformation dependent library (CDL) restraints added in 565.5 milliseconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 44.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 18 removed outlier: 7.018A pdb=" N GLU A 13 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL B 16 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ALA B 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU B 13 " --> pdb=" O GLY C 14 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL C 16 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL B 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA C 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 29 removed outlier: 6.908A pdb=" N GLY A 25 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY B 25 " --> pdb=" O GLN C 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 34 through 40 removed outlier: 6.373A pdb=" N LYS A 34 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL B 37 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLY A 36 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 9.902A pdb=" N TYR B 39 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N LEU A 38 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS B 34 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL C 37 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY B 36 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N TYR C 39 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LEU B 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 52 removed outlier: 7.030A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS B 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY A 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY B 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N HIS C 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL C 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLY B 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 63 through 67 Processing sheet with id=AA7, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA8, first strand: chain 'A' and resid 74 through 78 Processing sheet with id=AA9, first strand: chain 'A' and resid 88 through 95 removed outlier: 6.332A pdb=" N ALA A 89 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR B 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA A 91 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N PHE B 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N GLY A 93 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA B 89 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N THR C 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 91 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N PHE C 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLY B 93 " --> pdb=" O PHE C 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 9 Processing sheet with id=AB2, first strand: chain 'F' and resid 12 through 18 removed outlier: 7.016A pdb=" N GLU F 13 " --> pdb=" O GLY G 14 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL G 16 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL F 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA G 18 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA F 17 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLU G 13 " --> pdb=" O GLY H 14 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL H 16 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL G 15 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ALA H 18 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA G 17 " --> pdb=" O ALA H 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 24 through 29 removed outlier: 6.908A pdb=" N GLY F 25 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY G 25 " --> pdb=" O GLN H 24 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 34 through 40 removed outlier: 6.374A pdb=" N LYS F 34 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL G 37 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLY F 36 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N TYR G 39 " --> pdb=" O GLY F 36 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N LEU F 38 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS G 34 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL H 37 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLY G 36 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N TYR H 39 " --> pdb=" O GLY G 36 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N LEU G 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 46 through 52 removed outlier: 7.030A pdb=" N GLY F 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS G 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL F 49 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL G 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLY F 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLY G 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N HIS H 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL G 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL H 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLY G 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 63 through 67 Processing sheet with id=AB7, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AB8, first strand: chain 'F' and resid 74 through 78 Processing sheet with id=AB9, first strand: chain 'F' and resid 88 through 95 removed outlier: 6.332A pdb=" N ALA F 89 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR G 92 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA F 91 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N PHE G 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N GLY F 93 " --> pdb=" O PHE G 94 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA G 89 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR H 92 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA G 91 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N PHE H 94 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N GLY G 93 " --> pdb=" O PHE H 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 72 hydrogen bonds defined for protein. 216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1362 1.34 - 1.45: 314 1.45 - 1.57: 2434 1.57 - 1.68: 0 1.68 - 1.80: 24 Bond restraints: 4134 Sorted by residual: bond pdb=" C ACE A 0 " pdb=" O ACE A 0 " ideal model delta sigma weight residual 1.199 1.228 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C ACE G 0 " pdb=" O ACE G 0 " ideal model delta sigma weight residual 1.199 1.228 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C ACE F 0 " pdb=" O ACE F 0 " ideal model delta sigma weight residual 1.199 1.227 -0.028 2.00e-02 2.50e+03 2.03e+00 bond pdb=" C ACE H 0 " pdb=" O ACE H 0 " ideal model delta sigma weight residual 1.199 1.227 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C ACE C 0 " pdb=" O ACE C 0 " ideal model delta sigma weight residual 1.199 1.227 -0.028 2.00e-02 2.50e+03 1.89e+00 ... (remaining 4129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.69: 4726 0.69 - 1.39: 676 1.39 - 2.08: 87 2.08 - 2.77: 49 2.77 - 3.46: 6 Bond angle restraints: 5544 Sorted by residual: angle pdb=" CA GLY G 7 " pdb=" C GLY G 7 " pdb=" N LEU G 8 " ideal model delta sigma weight residual 115.31 117.60 -2.29 1.28e+00 6.10e-01 3.21e+00 angle pdb=" CA GLY B 7 " pdb=" C GLY B 7 " pdb=" N LEU B 8 " ideal model delta sigma weight residual 115.31 117.55 -2.24 1.28e+00 6.10e-01 3.05e+00 angle pdb=" CA GLY A 7 " pdb=" C GLY A 7 " pdb=" N LEU A 8 " ideal model delta sigma weight residual 115.31 117.52 -2.21 1.28e+00 6.10e-01 2.99e+00 angle pdb=" CA GLY C 7 " pdb=" C GLY C 7 " pdb=" N LEU C 8 " ideal model delta sigma weight residual 115.31 117.52 -2.21 1.28e+00 6.10e-01 2.97e+00 angle pdb=" N GLY G 7 " pdb=" CA GLY G 7 " pdb=" C GLY G 7 " ideal model delta sigma weight residual 110.20 112.47 -2.27 1.32e+00 5.74e-01 2.97e+00 ... (remaining 5539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2358 17.82 - 35.63: 90 35.63 - 53.45: 30 53.45 - 71.27: 0 71.27 - 89.08: 6 Dihedral angle restraints: 2484 sinusoidal: 888 harmonic: 1596 Sorted by residual: dihedral pdb=" CA GLU G 83 " pdb=" C GLU G 83 " pdb=" N GLY G 84 " pdb=" CA GLY G 84 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA GLU C 83 " pdb=" C GLU C 83 " pdb=" N GLY C 84 " pdb=" CA GLY C 84 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA GLU B 83 " pdb=" C GLU B 83 " pdb=" N GLY B 84 " pdb=" CA GLY B 84 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 2481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 386 0.034 - 0.068: 188 0.068 - 0.103: 68 0.103 - 0.137: 42 0.137 - 0.171: 6 Chirality restraints: 690 Sorted by residual: chirality pdb=" CG LEU C 8 " pdb=" CB LEU C 8 " pdb=" CD1 LEU C 8 " pdb=" CD2 LEU C 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CG LEU G 8 " pdb=" CB LEU G 8 " pdb=" CD1 LEU G 8 " pdb=" CD2 LEU G 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CG LEU F 8 " pdb=" CB LEU F 8 " pdb=" CD1 LEU F 8 " pdb=" CD2 LEU F 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 687 not shown) Planarity restraints: 696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 48 " 0.002 2.00e-02 2.50e+03 4.75e-03 2.26e-01 pdb=" C VAL H 48 " -0.008 2.00e-02 2.50e+03 pdb=" O VAL H 48 " 0.003 2.00e-02 2.50e+03 pdb=" N VAL H 49 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 67 " -0.002 2.00e-02 2.50e+03 4.73e-03 2.24e-01 pdb=" C GLY F 67 " 0.008 2.00e-02 2.50e+03 pdb=" O GLY F 67 " -0.003 2.00e-02 2.50e+03 pdb=" N GLY F 68 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 48 " -0.002 2.00e-02 2.50e+03 4.62e-03 2.14e-01 pdb=" C VAL A 48 " 0.008 2.00e-02 2.50e+03 pdb=" O VAL A 48 " -0.003 2.00e-02 2.50e+03 pdb=" N VAL A 49 " -0.003 2.00e-02 2.50e+03 ... (remaining 693 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 1429 2.87 - 3.38: 3320 3.38 - 3.89: 6207 3.89 - 4.39: 6611 4.39 - 4.90: 13776 Nonbonded interactions: 31343 Sorted by model distance: nonbonded pdb=" OD2 ASP B 2 " pdb=" NZ LYS B 10 " model vdw 2.368 3.120 nonbonded pdb=" OD2 ASP G 2 " pdb=" NZ LYS G 10 " model vdw 2.369 3.120 nonbonded pdb=" OD2 ASP A 2 " pdb=" NZ LYS A 10 " model vdw 2.369 3.120 nonbonded pdb=" OD2 ASP H 2 " pdb=" NZ LYS H 10 " model vdw 2.369 3.120 nonbonded pdb=" OD2 ASP C 2 " pdb=" NZ LYS C 10 " model vdw 2.369 3.120 ... (remaining 31338 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 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 2.530 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: 0.030 Set scattering table: 0.050 Process input model: 14.030 Find NCS groups from input model: 0.150 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 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 : 0.007 0.029 4134 Z= 0.480 Angle : 0.545 3.463 5544 Z= 0.326 Chirality : 0.052 0.171 690 Planarity : 0.001 0.005 696 Dihedral : 12.258 89.081 1476 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: -4.52 (0.23), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.17), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS G 50 PHE 0.006 0.001 PHE G 4 TYR 0.005 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.464 Fit side-chains REVERT: C 34 LYS cc_start: 0.8821 (mttt) cc_final: 0.8611 (mttm) REVERT: F 21 LYS cc_start: 0.8738 (mttm) cc_final: 0.8256 (mtmt) REVERT: F 96 LYS cc_start: 0.7806 (ttmm) cc_final: 0.7425 (mttm) REVERT: F 97 LYS cc_start: 0.7477 (ptpt) cc_final: 0.7101 (tttp) REVERT: G 57 GLU cc_start: 0.7905 (tt0) cc_final: 0.7505 (tm-30) REVERT: G 96 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7740 (mttm) REVERT: G 97 LYS cc_start: 0.6963 (ptpt) cc_final: 0.6667 (tttt) REVERT: H 20 GLU cc_start: 0.8606 (tp30) cc_final: 0.8301 (mm-30) REVERT: H 21 LYS cc_start: 0.8762 (mttm) cc_final: 0.8468 (mttt) REVERT: H 96 LYS cc_start: 0.8337 (ttmm) cc_final: 0.7909 (mttm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1634 time to fit residues: 19.5738 Evaluate side-chains 78 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS C 50 HIS F 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4134 Z= 0.168 Angle : 0.453 3.219 5544 Z= 0.260 Chirality : 0.050 0.134 690 Planarity : 0.002 0.008 696 Dihedral : 5.002 16.144 600 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.72 % Allowed : 12.75 % Favored : 85.54 % 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: -3.72 (0.27), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.20), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.005 0.001 PHE C 4 TYR 0.007 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: F 21 LYS cc_start: 0.8760 (mttm) cc_final: 0.8292 (mtmt) REVERT: F 97 LYS cc_start: 0.7205 (ptpt) cc_final: 0.6821 (pttm) REVERT: G 79 GLN cc_start: 0.9269 (mt0) cc_final: 0.8872 (mt0) REVERT: G 96 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7564 (mttm) REVERT: G 97 LYS cc_start: 0.7021 (ptpt) cc_final: 0.6780 (tttt) REVERT: H 20 GLU cc_start: 0.8396 (tp30) cc_final: 0.8035 (mm-30) REVERT: H 21 LYS cc_start: 0.8661 (mttm) cc_final: 0.7448 (mmtt) REVERT: H 96 LYS cc_start: 0.8146 (ttmm) cc_final: 0.7749 (tptt) outliers start: 7 outliers final: 4 residues processed: 87 average time/residue: 0.1627 time to fit residues: 17.9734 Evaluate side-chains 87 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.039 4134 Z= 0.516 Angle : 0.577 3.986 5544 Z= 0.325 Chirality : 0.052 0.123 690 Planarity : 0.002 0.008 696 Dihedral : 5.518 21.114 600 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.41 % Allowed : 12.50 % Favored : 83.09 % 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: -3.64 (0.27), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.21), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 50 PHE 0.006 0.001 PHE C 94 TYR 0.010 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.8823 (ttm) cc_final: 0.8587 (ttm) REVERT: F 13 GLU cc_start: 0.8624 (mp0) cc_final: 0.7974 (mp0) REVERT: F 20 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8559 (mm-30) REVERT: F 21 LYS cc_start: 0.8801 (mttm) cc_final: 0.8220 (mtmt) REVERT: F 57 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7500 (tm-30) REVERT: F 97 LYS cc_start: 0.7315 (ptpt) cc_final: 0.6905 (pttm) REVERT: G 57 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7290 (tm-30) REVERT: G 58 LYS cc_start: 0.9173 (mttt) cc_final: 0.8378 (mttp) REVERT: G 96 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7536 (mttm) REVERT: G 97 LYS cc_start: 0.7303 (ptpt) cc_final: 0.6962 (tttt) REVERT: H 20 GLU cc_start: 0.8571 (tp30) cc_final: 0.8279 (mm-30) REVERT: H 21 LYS cc_start: 0.8722 (mttm) cc_final: 0.7527 (mmtt) REVERT: H 96 LYS cc_start: 0.8259 (ttmm) cc_final: 0.7901 (tptt) outliers start: 18 outliers final: 15 residues processed: 94 average time/residue: 0.1521 time to fit residues: 17.9280 Evaluate side-chains 96 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 83 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 4134 Z= 0.247 Angle : 0.470 3.439 5544 Z= 0.268 Chirality : 0.050 0.130 690 Planarity : 0.001 0.008 696 Dihedral : 5.219 18.397 600 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.39 % Allowed : 13.24 % Favored : 81.37 % 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: -3.36 (0.29), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.003 0.001 PHE C 4 TYR 0.007 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: F 13 GLU cc_start: 0.8593 (mp0) cc_final: 0.7996 (mp0) REVERT: F 20 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8613 (mm-30) REVERT: F 21 LYS cc_start: 0.8778 (mttm) cc_final: 0.8180 (mtmt) REVERT: F 97 LYS cc_start: 0.7209 (ptpt) cc_final: 0.6747 (pttm) REVERT: G 3 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8371 (t) REVERT: G 58 LYS cc_start: 0.9182 (mttt) cc_final: 0.8776 (mttp) REVERT: G 96 LYS cc_start: 0.8106 (ttmm) cc_final: 0.7528 (mttm) REVERT: G 97 LYS cc_start: 0.7253 (ptpt) cc_final: 0.6922 (tttp) REVERT: H 21 LYS cc_start: 0.8718 (mttm) cc_final: 0.7417 (mmtt) REVERT: H 57 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: H 96 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7887 (tptt) outliers start: 22 outliers final: 14 residues processed: 92 average time/residue: 0.1503 time to fit residues: 17.5547 Evaluate side-chains 93 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 HIS F 50 HIS H 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4134 Z= 0.400 Angle : 0.525 3.730 5544 Z= 0.298 Chirality : 0.051 0.126 690 Planarity : 0.002 0.010 696 Dihedral : 5.376 19.553 600 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.64 % Allowed : 14.22 % Favored : 80.15 % 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 (0.29), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS H 50 PHE 0.022 0.001 PHE A 4 TYR 0.008 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: F 13 GLU cc_start: 0.8605 (mp0) cc_final: 0.7938 (mp0) REVERT: F 20 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8548 (mm-30) REVERT: F 21 LYS cc_start: 0.8789 (mttm) cc_final: 0.8185 (mtmt) REVERT: F 57 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7459 (tm-30) REVERT: F 97 LYS cc_start: 0.7259 (ptpt) cc_final: 0.6755 (pttm) REVERT: G 58 LYS cc_start: 0.9210 (mttt) cc_final: 0.8967 (mttp) REVERT: G 96 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7568 (mttm) REVERT: G 97 LYS cc_start: 0.7327 (ptpt) cc_final: 0.6983 (tttp) REVERT: H 21 LYS cc_start: 0.8770 (mttm) cc_final: 0.7489 (mmtt) REVERT: H 57 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: H 96 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7924 (tptt) outliers start: 23 outliers final: 18 residues processed: 91 average time/residue: 0.1522 time to fit residues: 17.5885 Evaluate side-chains 97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 4134 Z= 0.572 Angle : 0.610 4.838 5544 Z= 0.345 Chirality : 0.053 0.127 690 Planarity : 0.002 0.009 696 Dihedral : 5.708 21.851 600 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 6.37 % Allowed : 13.97 % Favored : 79.66 % 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: -3.41 (0.29), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS F 50 PHE 0.014 0.002 PHE A 4 TYR 0.009 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: F 13 GLU cc_start: 0.8626 (mp0) cc_final: 0.7885 (mp0) REVERT: F 20 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8477 (mm-30) REVERT: F 21 LYS cc_start: 0.8819 (mttm) cc_final: 0.8171 (mtmt) REVERT: F 57 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7483 (tm-30) REVERT: F 97 LYS cc_start: 0.7264 (ptpt) cc_final: 0.6777 (pttm) REVERT: G 58 LYS cc_start: 0.9221 (mttt) cc_final: 0.8981 (mttp) REVERT: G 96 LYS cc_start: 0.8100 (ttmm) cc_final: 0.7528 (mttm) REVERT: G 97 LYS cc_start: 0.7412 (ptpt) cc_final: 0.7151 (tttt) REVERT: H 96 LYS cc_start: 0.8171 (ttmm) cc_final: 0.7961 (tptt) outliers start: 26 outliers final: 21 residues processed: 95 average time/residue: 0.1414 time to fit residues: 17.2559 Evaluate side-chains 100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 83 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 HIS F 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4134 Z= 0.261 Angle : 0.490 3.996 5544 Z= 0.278 Chirality : 0.050 0.131 690 Planarity : 0.001 0.007 696 Dihedral : 5.379 20.388 600 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.90 % Allowed : 15.69 % Favored : 79.41 % 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: -3.25 (0.30), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 50 PHE 0.012 0.001 PHE A 4 TYR 0.005 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: F 13 GLU cc_start: 0.8566 (mp0) cc_final: 0.7917 (mp0) REVERT: F 20 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8586 (mm-30) REVERT: F 21 LYS cc_start: 0.8804 (mttm) cc_final: 0.8170 (mtmt) REVERT: F 57 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7455 (tm-30) REVERT: F 97 LYS cc_start: 0.7241 (ptpt) cc_final: 0.6716 (pttm) REVERT: G 5 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7157 (mmm) REVERT: G 58 LYS cc_start: 0.9222 (mttt) cc_final: 0.8994 (mttp) REVERT: G 96 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7530 (mttm) REVERT: G 97 LYS cc_start: 0.7356 (ptpt) cc_final: 0.7080 (tttt) REVERT: H 57 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: H 96 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7929 (tptt) outliers start: 20 outliers final: 17 residues processed: 87 average time/residue: 0.1504 time to fit residues: 16.7497 Evaluate side-chains 97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 64 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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: 0.8769 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 4134 Z= 0.485 Angle : 0.573 4.714 5544 Z= 0.323 Chirality : 0.052 0.127 690 Planarity : 0.002 0.007 696 Dihedral : 5.643 21.195 600 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.88 % Allowed : 15.44 % Favored : 78.68 % 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 (0.29), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 50 PHE 0.010 0.001 PHE A 4 TYR 0.007 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: F 13 GLU cc_start: 0.8606 (mp0) cc_final: 0.7892 (mp0) REVERT: F 20 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8463 (mm-30) REVERT: F 21 LYS cc_start: 0.8806 (mttm) cc_final: 0.8159 (mtmt) REVERT: F 57 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7507 (tm-30) REVERT: F 97 LYS cc_start: 0.7254 (ptpt) cc_final: 0.6779 (pttm) REVERT: G 5 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7249 (mmm) REVERT: G 58 LYS cc_start: 0.9228 (mttt) cc_final: 0.8976 (mttp) REVERT: G 96 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7498 (mttm) REVERT: G 97 LYS cc_start: 0.7483 (ptpt) cc_final: 0.7228 (tttt) REVERT: H 57 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: H 96 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7952 (tptt) outliers start: 24 outliers final: 19 residues processed: 94 average time/residue: 0.1408 time to fit residues: 17.0775 Evaluate side-chains 101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 83 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 45 optimal weight: 0.0570 chunk 48 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4134 Z= 0.315 Angle : 0.514 4.174 5544 Z= 0.291 Chirality : 0.051 0.130 690 Planarity : 0.002 0.011 696 Dihedral : 5.431 22.540 600 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.15 % Allowed : 16.18 % Favored : 78.68 % 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 (0.30), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 50 PHE 0.024 0.002 PHE B 4 TYR 0.006 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: F 13 GLU cc_start: 0.8573 (mp0) cc_final: 0.7910 (mp0) REVERT: F 20 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8582 (mm-30) REVERT: F 21 LYS cc_start: 0.8807 (mttm) cc_final: 0.8169 (mtmt) REVERT: F 57 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7492 (tm-30) REVERT: F 97 LYS cc_start: 0.7253 (ptpt) cc_final: 0.6755 (pttm) REVERT: G 5 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7234 (mmm) REVERT: G 58 LYS cc_start: 0.9222 (mttt) cc_final: 0.8945 (mttp) REVERT: G 96 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7522 (mttm) REVERT: G 97 LYS cc_start: 0.7459 (ptpt) cc_final: 0.7185 (tttp) REVERT: H 57 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7605 (tm-30) outliers start: 21 outliers final: 18 residues processed: 88 average time/residue: 0.1539 time to fit residues: 17.4690 Evaluate side-chains 97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.8733 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4134 Z= 0.262 Angle : 0.492 4.198 5544 Z= 0.279 Chirality : 0.050 0.130 690 Planarity : 0.001 0.010 696 Dihedral : 5.286 21.298 600 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.66 % Allowed : 16.42 % Favored : 78.92 % 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: -3.14 (0.30), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.022 0.002 PHE B 4 TYR 0.005 0.001 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: F 13 GLU cc_start: 0.8549 (mp0) cc_final: 0.7918 (mp0) REVERT: F 20 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8601 (mm-30) REVERT: F 21 LYS cc_start: 0.8785 (mttm) cc_final: 0.8148 (mtmt) REVERT: F 57 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7438 (tm-30) REVERT: F 97 LYS cc_start: 0.7250 (ptpt) cc_final: 0.6752 (pttm) REVERT: G 5 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7253 (mmm) REVERT: G 96 LYS cc_start: 0.7921 (ttmm) cc_final: 0.7497 (mttm) REVERT: G 97 LYS cc_start: 0.7506 (ptpt) cc_final: 0.7193 (tttp) REVERT: H 57 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7586 (tm-30) outliers start: 19 outliers final: 17 residues processed: 87 average time/residue: 0.1426 time to fit residues: 15.9179 Evaluate side-chains 95 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 49 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.104410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.094419 restraints weight = 5660.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.096814 restraints weight = 2596.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098304 restraints weight = 1509.885| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4134 Z= 0.252 Angle : 0.484 4.120 5544 Z= 0.274 Chirality : 0.050 0.129 690 Planarity : 0.001 0.009 696 Dihedral : 5.209 20.660 600 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.66 % Allowed : 16.18 % Favored : 79.17 % 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: -3.08 (0.30), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 50 PHE 0.019 0.002 PHE B 4 TYR 0.005 0.001 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1208.23 seconds wall clock time: 22 minutes 38.76 seconds (1358.76 seconds total)