Starting phenix.real_space_refine on Tue Feb 3 12:52:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kcp_62259/02_2026/9kcp_62259.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kcp_62259/02_2026/9kcp_62259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kcp_62259/02_2026/9kcp_62259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kcp_62259/02_2026/9kcp_62259.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kcp_62259/02_2026/9kcp_62259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kcp_62259/02_2026/9kcp_62259.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 3 Type Number sf(0) Gaussians C 1590 2.51 5 N 438 2.21 5 O 498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2526 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Restraints were copied for chains: E, F, G, H, I Time building chain proxies: 0.47, per 1000 atoms: 0.19 Number of scatterers: 2526 At special positions: 0 Unit cell: (103.75, 102.09, 30.71, 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 498 8.00 N 438 7.00 C 1590 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: 0.22 Conformation dependent library (CDL) restraints added in 121.6 milliseconds 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 63.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 38 through 41 Processing sheet with id=AA2, first strand: chain 'D' and resid 45 through 66 removed outlier: 8.495A pdb=" N GLU D 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL E 49 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N VAL D 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N GLY E 51 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N HIS D 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ALA E 53 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL D 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N VAL E 55 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR D 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLU E 57 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA D 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR E 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N LYS D 58 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLU E 61 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N LYS D 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N VAL E 63 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N GLN D 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 10.235A pdb=" N ASN E 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N THR D 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N GLU E 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N VAL F 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N VAL E 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.409A pdb=" N GLY F 51 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N HIS E 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ALA F 53 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL E 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL F 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR E 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLU F 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA E 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N THR F 59 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N LYS E 58 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLU F 61 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N LYS E 60 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N VAL F 63 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N GLN E 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 10.235A pdb=" N ASN F 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N THR E 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 69 through 82 removed outlier: 6.899A pdb=" N VAL E 70 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL D 71 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR E 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY D 73 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL D 77 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA E 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN D 79 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS E 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR D 81 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL E 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL F 70 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL E 71 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR F 72 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLY E 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL E 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA F 78 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLN E 79 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS F 80 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR E 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL F 82 " --> pdb=" O THR E 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AA5, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AA6, first strand: chain 'G' and resid 38 through 41 Processing sheet with id=AA7, first strand: chain 'G' and resid 45 through 66 removed outlier: 8.494A pdb=" N GLU G 46 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL H 49 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N VAL G 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N GLY H 51 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N HIS G 50 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N ALA H 53 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL G 52 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N VAL H 55 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR G 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLU H 57 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA G 56 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR H 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N LYS G 58 " --> pdb=" O THR H 59 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLU H 61 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N LYS G 60 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N VAL H 63 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N GLN G 62 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 10.235A pdb=" N ASN H 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N THR G 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N GLU H 46 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N VAL I 49 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N VAL H 48 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 10.409A pdb=" N GLY I 51 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N HIS H 50 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ALA I 53 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL H 52 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL I 55 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR H 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLU I 57 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA H 56 " --> pdb=" O GLU I 57 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR I 59 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N LYS H 58 " --> pdb=" O THR I 59 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLU I 61 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N LYS H 60 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N VAL I 63 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N GLN H 62 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N ASN I 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N THR H 64 " --> pdb=" O ASN I 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 69 through 82 removed outlier: 6.899A pdb=" N VAL H 70 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL G 71 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR H 72 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY G 73 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL G 77 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA H 78 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN G 79 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS H 80 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR G 81 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL H 82 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL I 70 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL H 71 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR I 72 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLY H 73 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL H 77 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA I 78 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN H 79 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS I 80 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR H 81 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL I 82 " --> pdb=" O THR H 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 86 through 87 Processing sheet with id=AB1, first strand: chain 'G' and resid 91 through 92 32 hydrogen bonds defined for protein. 96 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: 0.19 Time building geometry restraints manager: 0.29 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: 432 1.29 - 1.35: 390 1.35 - 1.42: 102 1.42 - 1.48: 420 1.48 - 1.54: 1194 Bond restraints: 2538 Sorted by residual: bond pdb=" CB GLN E 79 " pdb=" CG GLN E 79 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.84e-01 bond pdb=" CB GLN I 79 " pdb=" CG GLN I 79 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.60e-01 bond pdb=" CB GLN G 79 " pdb=" CG GLN G 79 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.59e-01 bond pdb=" CB GLN D 79 " pdb=" CG GLN D 79 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.24e-01 bond pdb=" CB GLN F 79 " pdb=" CG GLN F 79 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 7.95e-01 ... (remaining 2533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.80: 2991 0.80 - 1.59: 379 1.59 - 2.39: 49 2.39 - 3.18: 1 3.18 - 3.98: 12 Bond angle restraints: 3432 Sorted by residual: angle pdb=" C SER D 87 " pdb=" N ILE D 88 " pdb=" CA ILE D 88 " ideal model delta sigma weight residual 121.97 117.99 3.98 1.80e+00 3.09e-01 4.89e+00 angle pdb=" C SER G 87 " pdb=" N ILE G 88 " pdb=" CA ILE G 88 " ideal model delta sigma weight residual 121.97 118.01 3.96 1.80e+00 3.09e-01 4.83e+00 angle pdb=" C SER H 87 " pdb=" N ILE H 88 " pdb=" CA ILE H 88 " ideal model delta sigma weight residual 121.97 118.03 3.94 1.80e+00 3.09e-01 4.79e+00 angle pdb=" C SER E 87 " pdb=" N ILE E 88 " pdb=" CA ILE E 88 " ideal model delta sigma weight residual 121.97 118.04 3.93 1.80e+00 3.09e-01 4.77e+00 angle pdb=" C SER F 87 " pdb=" N ILE F 88 " pdb=" CA ILE F 88 " ideal model delta sigma weight residual 121.97 118.06 3.91 1.80e+00 3.09e-01 4.73e+00 ... (remaining 3427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.69: 1356 11.69 - 23.39: 108 23.39 - 35.08: 6 35.08 - 46.77: 6 46.77 - 58.47: 6 Dihedral angle restraints: 1482 sinusoidal: 492 harmonic: 990 Sorted by residual: dihedral pdb=" CA SER D 42 " pdb=" C SER D 42 " pdb=" N LYS D 43 " pdb=" CA LYS D 43 " ideal model delta harmonic sigma weight residual -180.00 -166.43 -13.57 0 5.00e+00 4.00e-02 7.36e+00 dihedral pdb=" CA SER H 42 " pdb=" C SER H 42 " pdb=" N LYS H 43 " pdb=" CA LYS H 43 " ideal model delta harmonic sigma weight residual -180.00 -166.44 -13.56 0 5.00e+00 4.00e-02 7.35e+00 dihedral pdb=" CA SER I 42 " pdb=" C SER I 42 " pdb=" N LYS I 43 " pdb=" CA LYS I 43 " ideal model delta harmonic sigma weight residual -180.00 -166.45 -13.55 0 5.00e+00 4.00e-02 7.35e+00 ... (remaining 1479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 194 0.024 - 0.049: 150 0.049 - 0.073: 26 0.073 - 0.097: 32 0.097 - 0.121: 54 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA VAL F 49 " pdb=" N VAL F 49 " pdb=" C VAL F 49 " pdb=" CB VAL F 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA VAL F 55 " pdb=" N VAL F 55 " pdb=" C VAL F 55 " pdb=" CB VAL F 55 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 453 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 50 " 0.006 2.00e-02 2.50e+03 5.62e-03 4.73e-01 pdb=" CG HIS D 50 " -0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS D 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS D 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS D 50 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS D 50 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS I 50 " -0.006 2.00e-02 2.50e+03 5.56e-03 4.64e-01 pdb=" CG HIS I 50 " 0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS I 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS I 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS I 50 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS I 50 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 50 " 0.006 2.00e-02 2.50e+03 5.52e-03 4.57e-01 pdb=" CG HIS E 50 " -0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS E 50 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS E 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS E 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS E 50 " 0.001 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 856 2.87 - 3.38: 1973 3.38 - 3.89: 4176 3.89 - 4.39: 4098 4.39 - 4.90: 8942 Nonbonded interactions: 20045 Sorted by model distance: nonbonded pdb=" O SER I 42 " pdb=" N THR I 44 " model vdw 2.363 3.120 nonbonded pdb=" O SER E 42 " pdb=" N THR E 44 " model vdw 2.363 3.120 nonbonded pdb=" O SER D 42 " pdb=" N THR D 44 " model vdw 2.364 3.120 nonbonded pdb=" O SER G 42 " pdb=" N THR G 44 " model vdw 2.364 3.120 nonbonded pdb=" O SER H 42 " pdb=" N THR H 44 " model vdw 2.364 3.120 ... (remaining 20040 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.920 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 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 : 0.005 0.028 2538 Z= 0.235 Angle : 0.560 3.979 3432 Z= 0.317 Chirality : 0.052 0.121 456 Planarity : 0.002 0.006 420 Dihedral : 10.202 58.466 858 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.39), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 39 PHE 0.011 0.003 PHE H 94 HIS 0.005 0.003 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 2538) covalent geometry : angle 0.56013 ( 3432) hydrogen bonds : bond 0.10294 ( 32) hydrogen bonds : angle 7.15384 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.059 Fit side-chains REVERT: D 46 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7717 (mt-10) REVERT: I 61 GLU cc_start: 0.8140 (tt0) cc_final: 0.7919 (tt0) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.5619 time to fit residues: 51.2979 Evaluate side-chains 54 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN E 65 ASN F 65 ASN G 65 ASN H 65 ASN I 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.134141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.108785 restraints weight = 2803.562| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.75 r_work: 0.3465 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2538 Z= 0.119 Angle : 0.466 3.340 3432 Z= 0.263 Chirality : 0.052 0.125 456 Planarity : 0.002 0.009 420 Dihedral : 3.745 9.127 366 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.10 % Allowed : 12.79 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR E 39 PHE 0.009 0.002 PHE H 94 HIS 0.004 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 2538) covalent geometry : angle 0.46552 ( 3432) hydrogen bonds : bond 0.02404 ( 32) hydrogen bonds : angle 5.52073 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.059 Fit side-chains REVERT: G 46 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6211 (mt-10) outliers start: 8 outliers final: 1 residues processed: 58 average time/residue: 0.5505 time to fit residues: 32.4636 Evaluate side-chains 54 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 0.0980 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.129395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.103643 restraints weight = 2906.312| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.81 r_work: 0.3385 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2538 Z= 0.218 Angle : 0.569 4.505 3432 Z= 0.321 Chirality : 0.054 0.129 456 Planarity : 0.002 0.012 420 Dihedral : 4.281 9.226 366 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 4.65 % Allowed : 10.85 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR H 39 PHE 0.012 0.003 PHE H 94 HIS 0.006 0.004 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 2538) covalent geometry : angle 0.56946 ( 3432) hydrogen bonds : bond 0.02575 ( 32) hydrogen bonds : angle 5.29890 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.099 Fit side-chains REVERT: E 83 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: G 46 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: I 83 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8060 (mp0) outliers start: 12 outliers final: 3 residues processed: 55 average time/residue: 0.6907 time to fit residues: 38.6072 Evaluate side-chains 60 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 83 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 0.0170 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 0.0670 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.144956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.120191 restraints weight = 2796.857| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.73 r_work: 0.3668 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.013 2538 Z= 0.064 Angle : 0.372 3.012 3432 Z= 0.212 Chirality : 0.052 0.121 456 Planarity : 0.001 0.007 420 Dihedral : 3.285 9.029 366 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.49 % Allowed : 13.18 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR H 39 PHE 0.005 0.001 PHE H 94 HIS 0.002 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00126 ( 2538) covalent geometry : angle 0.37239 ( 3432) hydrogen bonds : bond 0.01756 ( 32) hydrogen bonds : angle 4.96939 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.093 Fit side-chains REVERT: E 46 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8382 (mt-10) REVERT: E 83 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8151 (mp0) REVERT: I 83 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7853 (mp0) outliers start: 9 outliers final: 0 residues processed: 68 average time/residue: 0.7819 time to fit residues: 53.9598 Evaluate side-chains 55 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain I residue 83 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.128655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.102576 restraints weight = 2857.688| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.81 r_work: 0.3359 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2538 Z= 0.259 Angle : 0.592 4.602 3432 Z= 0.333 Chirality : 0.055 0.129 456 Planarity : 0.003 0.011 420 Dihedral : 4.450 9.709 366 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 6.59 % Allowed : 15.50 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR H 39 PHE 0.013 0.004 PHE F 94 HIS 0.007 0.004 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00600 ( 2538) covalent geometry : angle 0.59204 ( 3432) hydrogen bonds : bond 0.02751 ( 32) hydrogen bonds : angle 5.16278 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.059 Fit side-chains REVERT: D 83 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: E 83 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8151 (mp0) REVERT: G 83 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: I 83 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8103 (mp0) outliers start: 17 outliers final: 7 residues processed: 62 average time/residue: 0.7374 time to fit residues: 46.4213 Evaluate side-chains 67 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.131288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.104981 restraints weight = 2909.146| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.82 r_work: 0.3393 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2538 Z= 0.182 Angle : 0.523 4.112 3432 Z= 0.295 Chirality : 0.053 0.128 456 Planarity : 0.002 0.010 420 Dihedral : 4.249 9.363 366 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.04 % Allowed : 17.44 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR E 39 PHE 0.010 0.003 PHE I 94 HIS 0.006 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 2538) covalent geometry : angle 0.52295 ( 3432) hydrogen bonds : bond 0.02487 ( 32) hydrogen bonds : angle 5.14544 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.061 Fit side-chains REVERT: E 83 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: G 46 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8074 (tp30) REVERT: G 83 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: I 83 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8085 (mp0) outliers start: 13 outliers final: 6 residues processed: 61 average time/residue: 0.7623 time to fit residues: 47.2439 Evaluate side-chains 66 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 16 optimal weight: 0.0370 chunk 12 optimal weight: 0.3980 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 overall best weight: 5.0864 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.128620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.102066 restraints weight = 2868.543| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.86 r_work: 0.3339 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 2538 Z= 0.298 Angle : 0.638 5.087 3432 Z= 0.359 Chirality : 0.057 0.129 456 Planarity : 0.003 0.013 420 Dihedral : 4.784 11.525 366 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 5.43 % Allowed : 17.44 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR H 39 PHE 0.013 0.004 PHE E 94 HIS 0.008 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00689 ( 2538) covalent geometry : angle 0.63845 ( 3432) hydrogen bonds : bond 0.02895 ( 32) hydrogen bonds : angle 5.25231 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.096 Fit side-chains REVERT: E 83 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: G 46 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8077 (tp30) REVERT: G 83 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: I 83 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8126 (mp0) outliers start: 14 outliers final: 6 residues processed: 61 average time/residue: 0.7832 time to fit residues: 48.5211 Evaluate side-chains 67 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.134972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.108647 restraints weight = 2874.084| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.83 r_work: 0.3455 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2538 Z= 0.121 Angle : 0.459 3.362 3432 Z= 0.259 Chirality : 0.052 0.127 456 Planarity : 0.002 0.009 420 Dihedral : 3.968 10.532 366 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.26 % Allowed : 18.22 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR H 39 PHE 0.008 0.002 PHE I 94 HIS 0.004 0.003 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2538) covalent geometry : angle 0.45897 ( 3432) hydrogen bonds : bond 0.02163 ( 32) hydrogen bonds : angle 5.11487 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.099 Fit side-chains REVERT: E 83 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: G 46 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8041 (tp30) REVERT: G 83 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8199 (mp0) outliers start: 11 outliers final: 6 residues processed: 62 average time/residue: 0.7196 time to fit residues: 45.3053 Evaluate side-chains 65 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.134496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.107935 restraints weight = 2882.435| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.83 r_work: 0.3435 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2538 Z= 0.140 Angle : 0.474 3.532 3432 Z= 0.267 Chirality : 0.052 0.126 456 Planarity : 0.002 0.010 420 Dihedral : 4.051 11.039 366 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.10 % Allowed : 19.38 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR H 39 PHE 0.009 0.002 PHE E 94 HIS 0.005 0.003 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 2538) covalent geometry : angle 0.47378 ( 3432) hydrogen bonds : bond 0.02230 ( 32) hydrogen bonds : angle 5.02560 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.062 Fit side-chains REVERT: E 83 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: G 46 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8097 (tp30) REVERT: G 83 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8180 (mp0) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.7630 time to fit residues: 46.4564 Evaluate side-chains 62 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 35 optimal weight: 0.3980 chunk 30 optimal weight: 6.9990 chunk 32 optimal weight: 0.0060 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 0.0040 chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.4610 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.137261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.110969 restraints weight = 2830.318| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.79 r_work: 0.3492 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2538 Z= 0.107 Angle : 0.432 3.230 3432 Z= 0.244 Chirality : 0.052 0.130 456 Planarity : 0.001 0.008 420 Dihedral : 3.852 11.486 366 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.71 % Allowed : 20.54 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR H 39 PHE 0.007 0.002 PHE I 94 HIS 0.004 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 2538) covalent geometry : angle 0.43178 ( 3432) hydrogen bonds : bond 0.02038 ( 32) hydrogen bonds : angle 4.98074 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.112 Fit side-chains REVERT: E 83 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: G 46 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8081 (tp30) REVERT: G 83 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8163 (mp0) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.8503 time to fit residues: 51.8037 Evaluate side-chains 64 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.129607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.103251 restraints weight = 2876.192| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.84 r_work: 0.3366 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2538 Z= 0.239 Angle : 0.585 4.728 3432 Z= 0.326 Chirality : 0.055 0.129 456 Planarity : 0.002 0.012 420 Dihedral : 4.657 14.517 366 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.49 % Allowed : 20.54 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR H 39 PHE 0.012 0.003 PHE I 94 HIS 0.007 0.004 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 2538) covalent geometry : angle 0.58458 ( 3432) hydrogen bonds : bond 0.02601 ( 32) hydrogen bonds : angle 5.07998 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1371.13 seconds wall clock time: 24 minutes 5.01 seconds (1445.01 seconds total)