Starting phenix.real_space_refine on Wed Mar 5 16:01:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uak_26427/03_2025/7uak_26427.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uak_26427/03_2025/7uak_26427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uak_26427/03_2025/7uak_26427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uak_26427/03_2025/7uak_26427.map" model { file = "/net/cci-nas-00/data/ceres_data/7uak_26427/03_2025/7uak_26427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uak_26427/03_2025/7uak_26427.cif" } resolution = 3.38 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= 0.004 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 1614 2.51 5 N 450 2.21 5 O 522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2586 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 431 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 61} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.72, per 1000 atoms: 0.67 Number of scatterers: 2586 At special positions: 0 Unit cell: (95.23, 112.35, 34.24, 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 522 8.00 N 450 7.00 C 1614 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: 0.54 Conformation dependent library (CDL) restraints added in 316.3 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 56 removed outlier: 8.984A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ALA C 56 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 56 removed outlier: 8.984A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ALA C 56 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N VAL E 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLY C 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N THR E 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU C 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ALA E 56 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL C 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 64 Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.204A pdb=" N ALA A 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR C 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL A 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA C 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N THR E 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL C 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.410A pdb=" N THR A 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR C 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 94 removed outlier: 8.104A pdb=" N ALA A 89 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR C 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N ALA A 91 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N PHE C 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY A 93 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LYS C 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA E 89 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA C 90 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N PHE C 94 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL E 95 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS C 96 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 49 through 56 removed outlier: 8.787A pdb=" N VAL B 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N VAL D 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLY B 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR D 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU B 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA D 56 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL D 52 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU F 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR D 54 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL F 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA D 56 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 64 Processing sheet with id=AB1, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.349A pdb=" N ALA B 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA D 69 " --> pdb=" O VAL F 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 76 removed outlier: 6.679A pdb=" N THR B 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR D 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AB4, first strand: chain 'B' and resid 88 through 96 removed outlier: 8.156A pdb=" N ALA B 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N THR D 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N ALA B 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N PHE D 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY B 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LYS D 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ALA D 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N THR F 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N ALA D 91 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N PHE F 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY D 93 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LYS F 96 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL D 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 16 hydrogen bonds defined for protein. 48 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: 0.55 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 456 1.28 - 1.35: 402 1.35 - 1.41: 96 1.41 - 1.48: 438 1.48 - 1.55: 1206 Bond restraints: 2598 Sorted by residual: bond pdb=" N GLU B 46 " pdb=" CA GLU B 46 " ideal model delta sigma weight residual 1.456 1.479 -0.023 1.25e-02 6.40e+03 3.39e+00 bond pdb=" N GLU A 46 " pdb=" CA GLU A 46 " ideal model delta sigma weight residual 1.456 1.479 -0.023 1.25e-02 6.40e+03 3.36e+00 bond pdb=" N GLU D 46 " pdb=" CA GLU D 46 " ideal model delta sigma weight residual 1.456 1.478 -0.023 1.25e-02 6.40e+03 3.31e+00 bond pdb=" N GLU E 46 " pdb=" CA GLU E 46 " ideal model delta sigma weight residual 1.456 1.478 -0.022 1.25e-02 6.40e+03 3.16e+00 bond pdb=" N GLU F 46 " pdb=" CA GLU F 46 " ideal model delta sigma weight residual 1.456 1.478 -0.022 1.25e-02 6.40e+03 3.15e+00 ... (remaining 2593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 3329 1.23 - 2.45: 127 2.45 - 3.68: 36 3.68 - 4.91: 6 4.91 - 6.13: 12 Bond angle restraints: 3510 Sorted by residual: angle pdb=" C GLU E 46 " pdb=" CA GLU E 46 " pdb=" CB GLU E 46 " ideal model delta sigma weight residual 109.64 115.00 -5.36 1.77e+00 3.19e-01 9.19e+00 angle pdb=" C GLU B 46 " pdb=" CA GLU B 46 " pdb=" CB GLU B 46 " ideal model delta sigma weight residual 109.64 115.00 -5.36 1.77e+00 3.19e-01 9.16e+00 angle pdb=" C GLU D 46 " pdb=" CA GLU D 46 " pdb=" CB GLU D 46 " ideal model delta sigma weight residual 109.64 114.99 -5.35 1.77e+00 3.19e-01 9.12e+00 angle pdb=" C GLU F 46 " pdb=" CA GLU F 46 " pdb=" CB GLU F 46 " ideal model delta sigma weight residual 109.64 114.97 -5.33 1.77e+00 3.19e-01 9.08e+00 angle pdb=" C GLU A 46 " pdb=" CA GLU A 46 " pdb=" CB GLU A 46 " ideal model delta sigma weight residual 109.64 114.97 -5.33 1.77e+00 3.19e-01 9.06e+00 ... (remaining 3505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.04: 1206 10.04 - 20.08: 204 20.08 - 30.12: 72 30.12 - 40.16: 24 40.16 - 50.20: 18 Dihedral angle restraints: 1524 sinusoidal: 516 harmonic: 1008 Sorted by residual: dihedral pdb=" CA GLU D 46 " pdb=" C GLU D 46 " pdb=" N GLY D 47 " pdb=" CA GLY D 47 " ideal model delta harmonic sigma weight residual -180.00 -156.27 -23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA GLU C 46 " pdb=" C GLU C 46 " pdb=" N GLY C 47 " pdb=" CA GLY C 47 " ideal model delta harmonic sigma weight residual -180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA GLU A 46 " pdb=" C GLU A 46 " pdb=" N GLY A 47 " pdb=" CA GLY A 47 " ideal model delta harmonic sigma weight residual -180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 1521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 310 0.035 - 0.071: 54 0.071 - 0.106: 48 0.106 - 0.141: 38 0.141 - 0.177: 6 Chirality restraints: 456 Sorted by residual: chirality pdb=" CB VAL E 77 " pdb=" CA VAL E 77 " pdb=" CG1 VAL E 77 " pdb=" CG2 VAL E 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CB VAL D 77 " pdb=" CA VAL D 77 " pdb=" CG1 VAL D 77 " pdb=" CG2 VAL D 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CB VAL C 77 " pdb=" CA VAL C 77 " pdb=" CG1 VAL C 77 " pdb=" CG2 VAL C 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.72e-01 ... (remaining 453 not shown) Planarity restraints: 438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 94 " 0.000 2.00e-02 2.50e+03 9.16e-03 1.47e+00 pdb=" CG PHE E 94 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE E 94 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE E 94 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE E 94 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE E 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 94 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 94 " 0.000 2.00e-02 2.50e+03 9.03e-03 1.43e+00 pdb=" CG PHE A 94 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 94 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 94 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 94 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 94 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " -0.001 2.00e-02 2.50e+03 8.95e-03 1.40e+00 pdb=" CG PHE B 94 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " 0.002 2.00e-02 2.50e+03 ... (remaining 435 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1110 2.91 - 3.40: 2293 3.40 - 3.90: 4080 3.90 - 4.40: 3915 4.40 - 4.90: 8123 Nonbonded interactions: 19521 Sorted by model distance: nonbonded pdb=" N ASP B 98 " pdb=" OD1 ASP B 98 " model vdw 2.407 3.120 nonbonded pdb=" N ASP C 98 " pdb=" OD1 ASP C 98 " model vdw 2.407 3.120 nonbonded pdb=" N ASP D 98 " pdb=" OD1 ASP D 98 " model vdw 2.407 3.120 nonbonded pdb=" N ASP E 98 " pdb=" OD1 ASP E 98 " model vdw 2.407 3.120 nonbonded pdb=" N ASP F 98 " pdb=" OD1 ASP F 98 " model vdw 2.407 3.120 ... (remaining 19516 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.670 Find NCS groups from input model: 0.060 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 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 : 0.003 0.042 2598 Z= 0.234 Angle : 0.696 6.133 3510 Z= 0.404 Chirality : 0.053 0.177 456 Planarity : 0.002 0.010 438 Dihedral : 13.749 50.196 888 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.44 % Favored : 85.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.015 0.007 PHE E 94 TYR 0.001 0.000 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.286 Fit side-chains REVERT: E 79 GLN cc_start: 0.8009 (mp10) cc_final: 0.7802 (mp10) REVERT: F 57 GLU cc_start: 0.7570 (mp0) cc_final: 0.6840 (tm-30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1473 time to fit residues: 3.6382 Evaluate side-chains 16 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.141208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.105273 restraints weight = 3014.638| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 3.10 r_work: 0.3915 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2598 Z= 0.233 Angle : 0.618 5.559 3510 Z= 0.338 Chirality : 0.049 0.127 456 Planarity : 0.003 0.010 438 Dihedral : 6.015 25.949 372 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.50 % Favored : 82.50 % Rotamer: Outliers : 1.52 % Allowed : 4.17 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.39), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.010 0.003 PHE A 94 TYR 0.005 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.271 Fit side-chains REVERT: A 57 GLU cc_start: 0.7711 (mp0) cc_final: 0.7269 (mp0) REVERT: E 58 LYS cc_start: 0.7388 (ptpt) cc_final: 0.7091 (ptpt) outliers start: 4 outliers final: 4 residues processed: 26 average time/residue: 0.1378 time to fit residues: 4.5046 Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.132617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.097888 restraints weight = 3233.513| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.85 r_work: 0.3743 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 2598 Z= 0.531 Angle : 0.823 6.046 3510 Z= 0.462 Chirality : 0.059 0.183 456 Planarity : 0.004 0.013 438 Dihedral : 7.724 27.339 372 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.22 % Favored : 82.78 % Rotamer: Outliers : 4.55 % Allowed : 9.47 % Favored : 85.98 % 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: -3.75 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS B 50 PHE 0.007 0.002 PHE B 94 TYR 0.004 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7963 (mp0) cc_final: 0.7563 (mp0) REVERT: A 58 LYS cc_start: 0.7914 (ptpt) cc_final: 0.7452 (ptpt) REVERT: B 58 LYS cc_start: 0.8008 (ptpt) cc_final: 0.7793 (ptpt) REVERT: D 58 LYS cc_start: 0.7604 (pttt) cc_final: 0.7335 (ptpt) REVERT: E 57 GLU cc_start: 0.8155 (mp0) cc_final: 0.7863 (mp0) REVERT: E 58 LYS cc_start: 0.7534 (ptpt) cc_final: 0.7263 (ptpt) REVERT: F 58 LYS cc_start: 0.7343 (ptpt) cc_final: 0.7028 (ptpt) outliers start: 12 outliers final: 11 residues processed: 43 average time/residue: 0.2111 time to fit residues: 10.3825 Evaluate side-chains 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 77 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.142391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.107204 restraints weight = 3090.260| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.82 r_work: 0.3880 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2598 Z= 0.168 Angle : 0.569 4.797 3510 Z= 0.312 Chirality : 0.049 0.139 456 Planarity : 0.002 0.007 438 Dihedral : 6.288 25.580 372 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer: Outliers : 3.79 % Allowed : 11.36 % Favored : 84.85 % 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: -3.49 (0.36), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.004 0.001 PHE D 94 TYR 0.003 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.245 Fit side-chains REVERT: A 38 LEU cc_start: 0.4726 (OUTLIER) cc_final: 0.4344 (tt) REVERT: A 57 GLU cc_start: 0.7649 (mp0) cc_final: 0.7074 (mp0) REVERT: A 58 LYS cc_start: 0.7615 (ptpt) cc_final: 0.7360 (ptpt) REVERT: B 58 LYS cc_start: 0.7814 (ptpt) cc_final: 0.7608 (ptpt) REVERT: D 58 LYS cc_start: 0.7024 (pttt) cc_final: 0.6746 (ptpt) REVERT: E 38 LEU cc_start: 0.4349 (OUTLIER) cc_final: 0.3967 (tt) REVERT: E 57 GLU cc_start: 0.7943 (mp0) cc_final: 0.7557 (mp0) REVERT: F 38 LEU cc_start: 0.4579 (OUTLIER) cc_final: 0.3955 (tt) outliers start: 10 outliers final: 4 residues processed: 31 average time/residue: 0.1997 time to fit residues: 7.2655 Evaluate side-chains 29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.4333 r_free = 0.4333 target = 0.139139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.104287 restraints weight = 3092.696| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.84 r_work: 0.3824 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2598 Z= 0.235 Angle : 0.594 4.664 3510 Z= 0.327 Chirality : 0.049 0.133 456 Planarity : 0.002 0.008 438 Dihedral : 6.265 24.698 372 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.22 % Favored : 82.78 % Rotamer: Outliers : 6.06 % Allowed : 11.36 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.37), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 50 PHE 0.004 0.001 PHE D 94 TYR 0.002 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 24 time to evaluate : 0.251 Fit side-chains REVERT: A 38 LEU cc_start: 0.5049 (OUTLIER) cc_final: 0.4623 (tt) REVERT: A 57 GLU cc_start: 0.7729 (mp0) cc_final: 0.7068 (mp0) REVERT: A 65 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7654 (p0) REVERT: B 38 LEU cc_start: 0.4407 (OUTLIER) cc_final: 0.3633 (tt) REVERT: E 38 LEU cc_start: 0.4536 (OUTLIER) cc_final: 0.4111 (tt) REVERT: E 57 GLU cc_start: 0.7881 (mp0) cc_final: 0.7357 (mp0) REVERT: F 38 LEU cc_start: 0.4801 (OUTLIER) cc_final: 0.4136 (tt) REVERT: F 79 GLN cc_start: 0.8340 (mp10) cc_final: 0.8055 (mp10) outliers start: 16 outliers final: 9 residues processed: 36 average time/residue: 0.1845 time to fit residues: 7.7794 Evaluate side-chains 39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 0.0270 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.9440 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.136181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.099938 restraints weight = 3056.391| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.96 r_work: 0.3842 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2598 Z= 0.159 Angle : 0.545 4.417 3510 Z= 0.299 Chirality : 0.048 0.132 456 Planarity : 0.002 0.007 438 Dihedral : 5.889 23.981 372 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.17 % Favored : 85.83 % Rotamer: Outliers : 5.30 % Allowed : 14.39 % Favored : 80.30 % 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 (0.39), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.003 0.001 PHE D 94 TYR 0.003 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 21 time to evaluate : 0.287 Fit side-chains REVERT: A 38 LEU cc_start: 0.5078 (OUTLIER) cc_final: 0.4708 (tt) REVERT: A 57 GLU cc_start: 0.7784 (mp0) cc_final: 0.7109 (mp0) REVERT: A 65 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7538 (p0) REVERT: B 38 LEU cc_start: 0.4239 (OUTLIER) cc_final: 0.3439 (tt) REVERT: B 57 GLU cc_start: 0.7686 (mp0) cc_final: 0.7423 (mp0) REVERT: D 58 LYS cc_start: 0.7210 (pttt) cc_final: 0.6886 (ptpt) REVERT: E 38 LEU cc_start: 0.4295 (OUTLIER) cc_final: 0.3924 (tt) REVERT: E 57 GLU cc_start: 0.7766 (mp0) cc_final: 0.7144 (mp0) REVERT: F 38 LEU cc_start: 0.4207 (OUTLIER) cc_final: 0.3604 (tp) outliers start: 14 outliers final: 7 residues processed: 31 average time/residue: 0.1997 time to fit residues: 7.2859 Evaluate side-chains 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 21 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.128431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.093524 restraints weight = 3256.533| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.98 r_work: 0.3695 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2598 Z= 0.411 Angle : 0.693 5.050 3510 Z= 0.386 Chirality : 0.053 0.134 456 Planarity : 0.003 0.008 438 Dihedral : 6.882 24.694 372 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.33 % Favored : 81.67 % Rotamer: Outliers : 7.58 % Allowed : 13.64 % Favored : 78.79 % 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: -3.52 (0.36), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 50 PHE 0.005 0.002 PHE D 94 TYR 0.003 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 28 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.4984 (OUTLIER) cc_final: 0.4466 (tt) REVERT: A 57 GLU cc_start: 0.7783 (mp0) cc_final: 0.7157 (mp0) REVERT: A 58 LYS cc_start: 0.7735 (ptpt) cc_final: 0.7067 (ptpt) REVERT: B 38 LEU cc_start: 0.3945 (OUTLIER) cc_final: 0.3297 (tt) REVERT: D 58 LYS cc_start: 0.7526 (pttt) cc_final: 0.7304 (ptpt) REVERT: E 38 LEU cc_start: 0.4393 (OUTLIER) cc_final: 0.3865 (tt) REVERT: E 57 GLU cc_start: 0.7721 (mp0) cc_final: 0.7214 (mp0) REVERT: F 38 LEU cc_start: 0.4649 (OUTLIER) cc_final: 0.4074 (tt) REVERT: F 79 GLN cc_start: 0.8441 (mp10) cc_final: 0.8217 (mp10) outliers start: 20 outliers final: 11 residues processed: 45 average time/residue: 0.2105 time to fit residues: 10.8456 Evaluate side-chains 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 77 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.4341 r_free = 0.4341 target = 0.137752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.101307 restraints weight = 3042.499| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.96 r_work: 0.3853 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2598 Z= 0.136 Angle : 0.545 4.464 3510 Z= 0.297 Chirality : 0.048 0.128 456 Planarity : 0.002 0.006 438 Dihedral : 5.808 22.096 372 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 4.17 % Allowed : 17.42 % Favored : 78.41 % 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: -3.22 (0.39), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.005 0.001 PHE D 94 TYR 0.003 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.301 Fit side-chains REVERT: A 38 LEU cc_start: 0.5116 (OUTLIER) cc_final: 0.4646 (tt) REVERT: A 57 GLU cc_start: 0.7801 (mp0) cc_final: 0.7129 (mp0) REVERT: A 58 LYS cc_start: 0.7445 (ptpt) cc_final: 0.7097 (ptpt) REVERT: B 38 LEU cc_start: 0.4530 (OUTLIER) cc_final: 0.3644 (tt) REVERT: D 58 LYS cc_start: 0.7260 (pttt) cc_final: 0.6901 (ptpt) REVERT: E 38 LEU cc_start: 0.4022 (OUTLIER) cc_final: 0.3593 (tt) REVERT: E 57 GLU cc_start: 0.7753 (mp0) cc_final: 0.7171 (mp0) REVERT: F 38 LEU cc_start: 0.4125 (OUTLIER) cc_final: 0.3503 (tt) outliers start: 11 outliers final: 6 residues processed: 33 average time/residue: 0.2324 time to fit residues: 8.8394 Evaluate side-chains 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4292 r_free = 0.4292 target = 0.133774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.098037 restraints weight = 3114.309| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.93 r_work: 0.3794 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2598 Z= 0.214 Angle : 0.579 4.283 3510 Z= 0.317 Chirality : 0.049 0.125 456 Planarity : 0.002 0.010 438 Dihedral : 5.914 21.708 372 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.11 % Favored : 83.89 % Rotamer: Outliers : 4.55 % Allowed : 17.42 % Favored : 78.03 % 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: -3.23 (0.39), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS D 50 PHE 0.004 0.001 PHE D 94 TYR 0.002 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.5377 (OUTLIER) cc_final: 0.4894 (tt) REVERT: A 57 GLU cc_start: 0.7731 (mp0) cc_final: 0.7040 (mp0) REVERT: A 58 LYS cc_start: 0.7522 (ptpt) cc_final: 0.7151 (ptpt) REVERT: B 38 LEU cc_start: 0.4297 (OUTLIER) cc_final: 0.3410 (tt) REVERT: D 58 LYS cc_start: 0.7264 (pttt) cc_final: 0.6898 (ptpt) REVERT: E 38 LEU cc_start: 0.4318 (OUTLIER) cc_final: 0.3905 (tt) REVERT: E 57 GLU cc_start: 0.7834 (mp0) cc_final: 0.7240 (mp0) REVERT: E 79 GLN cc_start: 0.8580 (mp10) cc_final: 0.8092 (mp10) REVERT: F 38 LEU cc_start: 0.4472 (OUTLIER) cc_final: 0.3820 (tp) REVERT: F 79 GLN cc_start: 0.8454 (mp10) cc_final: 0.8005 (mp10) outliers start: 12 outliers final: 7 residues processed: 38 average time/residue: 0.2250 time to fit residues: 9.7990 Evaluate side-chains 39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 35 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.134307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.098297 restraints weight = 3050.207| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.92 r_work: 0.3808 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2598 Z= 0.200 Angle : 0.578 4.210 3510 Z= 0.316 Chirality : 0.049 0.128 456 Planarity : 0.002 0.010 438 Dihedral : 5.918 22.604 372 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.28 % Favored : 84.72 % Rotamer: Outliers : 4.92 % Allowed : 17.05 % Favored : 78.03 % 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: -3.22 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.004 0.001 PHE D 94 TYR 0.002 0.001 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.269 Fit side-chains REVERT: A 38 LEU cc_start: 0.5308 (OUTLIER) cc_final: 0.4858 (tt) REVERT: A 57 GLU cc_start: 0.7731 (mp0) cc_final: 0.6995 (mp0) REVERT: A 58 LYS cc_start: 0.7474 (ptpt) cc_final: 0.7103 (ptpt) REVERT: B 38 LEU cc_start: 0.4590 (OUTLIER) cc_final: 0.3696 (tt) REVERT: D 58 LYS cc_start: 0.7223 (pttt) cc_final: 0.6861 (ptpt) REVERT: E 38 LEU cc_start: 0.4039 (OUTLIER) cc_final: 0.3653 (tt) REVERT: E 57 GLU cc_start: 0.7830 (mp0) cc_final: 0.7229 (mp0) REVERT: F 38 LEU cc_start: 0.4295 (OUTLIER) cc_final: 0.3556 (tt) REVERT: F 79 GLN cc_start: 0.8418 (mp10) cc_final: 0.8068 (mp10) outliers start: 13 outliers final: 7 residues processed: 38 average time/residue: 0.2235 time to fit residues: 9.7428 Evaluate side-chains 38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.130699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.095577 restraints weight = 3166.966| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.94 r_work: 0.3725 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2598 Z= 0.295 Angle : 0.638 4.954 3510 Z= 0.350 Chirality : 0.050 0.125 456 Planarity : 0.002 0.010 438 Dihedral : 6.317 22.935 372 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.06 % Favored : 81.94 % Rotamer: Outliers : 4.92 % Allowed : 17.05 % Favored : 78.03 % 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 (0.38), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.003 HIS B 50 PHE 0.004 0.001 PHE D 94 TYR 0.003 0.001 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.23 seconds wall clock time: 32 minutes 44.93 seconds (1964.93 seconds total)