Starting phenix.real_space_refine on Fri Aug 22 13:12:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yk8_33890/08_2025/7yk8_33890.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yk8_33890/08_2025/7yk8_33890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yk8_33890/08_2025/7yk8_33890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yk8_33890/08_2025/7yk8_33890.map" model { file = "/net/cci-nas-00/data/ceres_data/7yk8_33890/08_2025/7yk8_33890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yk8_33890/08_2025/7yk8_33890.cif" } resolution = 2.8 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= 0.004 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 1938 2.51 5 N 546 2.21 5 O 624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3108 Number of models: 1 Model: "" Number of chains: 2 Chain: "L" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Restraints were copied for chains: B, J, E, K, F, A, G, C, H, D Time building chain proxies: 0.51, per 1000 atoms: 0.16 Number of scatterers: 3108 At special positions: 0 Unit cell: (94.34, 117.66, 32.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 624 8.00 N 546 7.00 C 1938 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.16 Conformation dependent library (CDL) restraints added in 93.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'J' and resid 46 through 57 removed outlier: 6.878A pdb=" N VAL J 48 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL L 49 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N HIS J 50 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY L 51 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N GLU L 46 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N VAL K 49 " --> pdb=" O GLU L 46 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N VAL L 48 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N GLY K 51 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N HIS L 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N ALA K 53 " --> pdb=" O HIS L 50 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL L 52 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL K 55 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR L 54 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU K 57 " --> pdb=" O THR L 54 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA L 56 " --> pdb=" O GLU K 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 61 through 66 removed outlier: 6.312A pdb=" N GLN L 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASN J 65 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR L 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 69 through 82 removed outlier: 6.597A pdb=" N ALA L 69 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N THR J 72 " --> pdb=" O ALA L 69 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL L 71 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL J 74 " --> pdb=" O VAL L 71 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLY L 73 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N ALA J 76 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR L 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ALA J 78 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL L 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N LYS J 80 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN L 79 " --> pdb=" O LYS J 80 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N VAL J 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR L 81 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL L 74 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR K 75 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA L 76 " --> pdb=" O THR K 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 86 through 92 removed outlier: 6.976A pdb=" N SER L 87 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE J 88 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N GLY L 86 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N ALA K 89 " --> pdb=" O GLY L 86 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE L 88 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA K 91 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA L 90 " --> pdb=" O ALA K 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 16 through 18 removed outlier: 6.225A pdb=" N VAL I 16 " --> pdb=" O ALA H 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 46 through 57 removed outlier: 6.883A pdb=" N VAL E 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS E 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY B 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N GLU B 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N VAL F 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N VAL B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N GLY F 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS B 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N ALA F 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL B 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N VAL F 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR B 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU F 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA B 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 61 through 66 removed outlier: 6.310A pdb=" N GLN B 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASN E 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR B 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 82 removed outlier: 6.598A pdb=" N ALA B 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N THR E 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL E 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLY B 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ALA E 76 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THR B 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ALA E 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LYS E 80 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN B 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N VAL E 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR B 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL B 74 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR F 75 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA B 76 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 92 removed outlier: 6.980A pdb=" N SER B 87 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE E 88 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLY B 86 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N ALA F 89 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE B 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA F 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA B 90 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 18 removed outlier: 6.220A pdb=" N VAL A 16 " --> pdb=" O ALA D 17 " (cutoff:3.500A) 56 hydrogen bonds defined for protein. 168 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: 0.33 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 552 1.29 - 1.35: 482 1.35 - 1.42: 106 1.42 - 1.48: 498 1.48 - 1.55: 1476 Bond restraints: 3114 Sorted by residual: bond pdb=" N LEU E 38 " pdb=" CA LEU E 38 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.53e+00 bond pdb=" N LEU F 38 " pdb=" CA LEU F 38 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.50e+00 bond pdb=" N LEU L 38 " pdb=" CA LEU L 38 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.49e+00 bond pdb=" N LEU J 38 " pdb=" CA LEU J 38 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.49e+00 bond pdb=" N LEU K 38 " pdb=" CA LEU K 38 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.25e-02 6.40e+03 6.26e+00 ... (remaining 3109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.80: 3578 0.80 - 1.61: 463 1.61 - 2.41: 96 2.41 - 3.21: 45 3.21 - 4.02: 12 Bond angle restraints: 4194 Sorted by residual: angle pdb=" N LEU L 38 " pdb=" CA LEU L 38 " pdb=" C LEU L 38 " ideal model delta sigma weight residual 112.93 108.91 4.02 1.33e+00 5.65e-01 9.12e+00 angle pdb=" N LEU E 38 " pdb=" CA LEU E 38 " pdb=" C LEU E 38 " ideal model delta sigma weight residual 112.93 108.92 4.01 1.33e+00 5.65e-01 9.08e+00 angle pdb=" N LEU F 38 " pdb=" CA LEU F 38 " pdb=" C LEU F 38 " ideal model delta sigma weight residual 112.93 108.93 4.00 1.33e+00 5.65e-01 9.04e+00 angle pdb=" N LEU K 38 " pdb=" CA LEU K 38 " pdb=" C LEU K 38 " ideal model delta sigma weight residual 112.93 108.94 3.99 1.33e+00 5.65e-01 9.01e+00 angle pdb=" N LEU B 38 " pdb=" CA LEU B 38 " pdb=" C LEU B 38 " ideal model delta sigma weight residual 112.93 108.96 3.97 1.33e+00 5.65e-01 8.92e+00 ... (remaining 4189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.91: 1572 10.91 - 21.82: 192 21.82 - 32.73: 48 32.73 - 43.63: 12 43.63 - 54.54: 12 Dihedral angle restraints: 1836 sinusoidal: 624 harmonic: 1212 Sorted by residual: dihedral pdb=" N LYS F 45 " pdb=" CA LYS F 45 " pdb=" CB LYS F 45 " pdb=" CG LYS F 45 " ideal model delta sinusoidal sigma weight residual -180.00 -125.46 -54.54 3 1.50e+01 4.44e-03 9.29e+00 dihedral pdb=" N LYS J 45 " pdb=" CA LYS J 45 " pdb=" CB LYS J 45 " pdb=" CG LYS J 45 " ideal model delta sinusoidal sigma weight residual -180.00 -125.46 -54.54 3 1.50e+01 4.44e-03 9.29e+00 dihedral pdb=" N LYS L 45 " pdb=" CA LYS L 45 " pdb=" CB LYS L 45 " pdb=" CG LYS L 45 " ideal model delta sinusoidal sigma weight residual -180.00 -125.47 -54.53 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 1833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 261 0.033 - 0.067: 150 0.067 - 0.100: 50 0.100 - 0.134: 61 0.134 - 0.167: 24 Chirality restraints: 546 Sorted by residual: chirality pdb=" CA VAL E 37 " pdb=" N VAL E 37 " pdb=" C VAL E 37 " pdb=" CB VAL E 37 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA VAL F 37 " pdb=" N VAL F 37 " pdb=" C VAL F 37 " pdb=" CB VAL F 37 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA VAL L 37 " pdb=" N VAL L 37 " pdb=" C VAL L 37 " pdb=" CB VAL L 37 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 543 not shown) Planarity restraints: 522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL L 95 " -0.004 2.00e-02 2.50e+03 7.83e-03 6.13e-01 pdb=" C VAL L 95 " 0.014 2.00e-02 2.50e+03 pdb=" O VAL L 95 " -0.005 2.00e-02 2.50e+03 pdb=" N LYS L 96 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 95 " -0.004 2.00e-02 2.50e+03 7.80e-03 6.09e-01 pdb=" C VAL J 95 " 0.013 2.00e-02 2.50e+03 pdb=" O VAL J 95 " -0.005 2.00e-02 2.50e+03 pdb=" N LYS J 96 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 95 " -0.004 2.00e-02 2.50e+03 7.73e-03 5.97e-01 pdb=" C VAL F 95 " 0.013 2.00e-02 2.50e+03 pdb=" O VAL F 95 " -0.005 2.00e-02 2.50e+03 pdb=" N LYS F 96 " -0.004 2.00e-02 2.50e+03 ... (remaining 519 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 1354 2.95 - 3.44: 2895 3.44 - 3.93: 4431 3.93 - 4.41: 4982 4.41 - 4.90: 10182 Nonbonded interactions: 23844 Sorted by model distance: nonbonded pdb=" N VAL B 37 " pdb=" O VAL F 37 " model vdw 2.465 3.120 nonbonded pdb=" N VAL L 37 " pdb=" O VAL K 37 " model vdw 2.480 3.120 nonbonded pdb=" O VAL L 37 " pdb=" N VAL J 37 " model vdw 2.488 3.120 nonbonded pdb=" O VAL B 37 " pdb=" N VAL E 37 " model vdw 2.495 3.120 nonbonded pdb=" O ILE B 88 " pdb=" N ALA F 89 " model vdw 2.650 3.120 ... (remaining 23839 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 'L' selection = chain 'B' selection = chain 'J' selection = chain 'E' selection = chain 'K' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'A' selection = chain 'G' selection = chain 'C' selection = chain 'H' selection = chain 'D' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 3.850 Find NCS groups from input model: 0.030 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:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 0.036 3114 Z= 0.246 Angle : 0.661 4.016 4194 Z= 0.415 Chirality : 0.063 0.167 546 Planarity : 0.002 0.008 522 Dihedral : 11.560 54.540 1068 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR L 39 PHE 0.011 0.003 PHE K 94 HIS 0.004 0.002 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 3114) covalent geometry : angle 0.66096 ( 4194) hydrogen bonds : bond 0.23418 ( 56) hydrogen bonds : angle 9.23396 ( 168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.118 Fit side-chains REVERT: A 20 GLU cc_start: 0.7565 (tt0) cc_final: 0.7271 (tt0) REVERT: J 60 LYS cc_start: 0.8416 (tttt) cc_final: 0.8130 (tmtm) REVERT: G 20 GLU cc_start: 0.7482 (tt0) cc_final: 0.7044 (tt0) REVERT: E 43 LYS cc_start: 0.7492 (tppp) cc_final: 0.7288 (mmmm) REVERT: C 20 GLU cc_start: 0.7548 (tt0) cc_final: 0.7217 (tt0) REVERT: K 43 LYS cc_start: 0.7492 (tppp) cc_final: 0.7087 (mmmm) REVERT: F 43 LYS cc_start: 0.7536 (tppp) cc_final: 0.7163 (mmmt) REVERT: F 45 LYS cc_start: 0.8026 (tttt) cc_final: 0.7791 (ttmt) REVERT: D 20 GLU cc_start: 0.7446 (tt0) cc_final: 0.7127 (tm-30) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.4250 time to fit residues: 38.4205 Evaluate side-chains 77 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN J 50 HIS E 50 HIS F 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.193928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.151777 restraints weight = 3109.546| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.25 r_work: 0.3962 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3834 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3114 Z= 0.123 Angle : 0.511 3.718 4194 Z= 0.292 Chirality : 0.051 0.136 546 Planarity : 0.002 0.009 522 Dihedral : 4.336 11.833 444 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 7.37 % Allowed : 14.42 % Favored : 78.21 % 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 aren not related in a simple way. whole: -3.17 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR E 39 PHE 0.010 0.003 PHE F 94 HIS 0.003 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3114) covalent geometry : angle 0.51097 ( 4194) hydrogen bonds : bond 0.03027 ( 56) hydrogen bonds : angle 6.95414 ( 168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.130 Fit side-chains REVERT: B 45 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7419 (tttp) REVERT: A 20 GLU cc_start: 0.7937 (tt0) cc_final: 0.7590 (tt0) REVERT: J 60 LYS cc_start: 0.8782 (tttt) cc_final: 0.8373 (tmtm) REVERT: G 20 GLU cc_start: 0.7863 (tt0) cc_final: 0.7263 (tt0) REVERT: C 20 GLU cc_start: 0.7980 (tt0) cc_final: 0.7607 (tt0) REVERT: K 43 LYS cc_start: 0.7361 (tppp) cc_final: 0.6876 (mmmm) REVERT: K 60 LYS cc_start: 0.8493 (tttt) cc_final: 0.8284 (tmtp) REVERT: F 43 LYS cc_start: 0.7209 (tppp) cc_final: 0.6731 (mmmt) outliers start: 23 outliers final: 13 residues processed: 84 average time/residue: 0.4202 time to fit residues: 36.2986 Evaluate side-chains 93 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS B 65 ASN F 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.187606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.144335 restraints weight = 3131.524| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.27 r_work: 0.3862 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3114 Z= 0.259 Angle : 0.646 4.134 4194 Z= 0.382 Chirality : 0.055 0.153 546 Planarity : 0.003 0.013 522 Dihedral : 4.789 13.573 444 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 13.14 % Allowed : 12.82 % Favored : 74.04 % 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 aren not related in a simple way. whole: -3.29 (0.36), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR E 39 PHE 0.010 0.003 PHE E 94 HIS 0.006 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 3114) covalent geometry : angle 0.64601 ( 4194) hydrogen bonds : bond 0.03770 ( 56) hydrogen bonds : angle 6.92556 ( 168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 81 time to evaluate : 0.072 Fit side-chains REVERT: L 58 LYS cc_start: 0.7618 (mttt) cc_final: 0.7349 (mttt) REVERT: I 20 GLU cc_start: 0.7744 (tt0) cc_final: 0.7512 (tt0) REVERT: B 45 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8021 (ttmt) REVERT: B 60 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8189 (tmtp) REVERT: A 20 GLU cc_start: 0.7894 (tt0) cc_final: 0.7513 (tt0) REVERT: J 60 LYS cc_start: 0.8794 (tttt) cc_final: 0.8352 (tmtm) REVERT: G 20 GLU cc_start: 0.7941 (tt0) cc_final: 0.7369 (tt0) REVERT: E 60 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8124 (tmtp) REVERT: C 20 GLU cc_start: 0.8005 (tt0) cc_final: 0.7596 (tt0) REVERT: F 43 LYS cc_start: 0.7363 (tppp) cc_final: 0.6871 (mmmt) REVERT: F 83 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7988 (mt-10) outliers start: 41 outliers final: 26 residues processed: 91 average time/residue: 0.4985 time to fit residues: 46.5486 Evaluate side-chains 107 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain D residue 15 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.196384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.154301 restraints weight = 3081.865| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.21 r_work: 0.3993 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3114 Z= 0.106 Angle : 0.482 4.076 4194 Z= 0.282 Chirality : 0.050 0.131 546 Planarity : 0.002 0.009 522 Dihedral : 4.347 14.316 444 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 10.58 % Allowed : 14.42 % Favored : 75.00 % 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 aren not related in a simple way. whole: -2.95 (0.38), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR L 39 PHE 0.011 0.003 PHE B 94 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 3114) covalent geometry : angle 0.48213 ( 4194) hydrogen bonds : bond 0.02375 ( 56) hydrogen bonds : angle 6.49252 ( 168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.093 Fit side-chains REVERT: L 38 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5688 (tm) REVERT: I 20 GLU cc_start: 0.7722 (tt0) cc_final: 0.7487 (tt0) REVERT: B 61 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7946 (tp30) REVERT: A 20 GLU cc_start: 0.7905 (tt0) cc_final: 0.7513 (tt0) REVERT: J 38 LEU cc_start: 0.6135 (OUTLIER) cc_final: 0.5830 (tt) REVERT: J 60 LYS cc_start: 0.8754 (tttt) cc_final: 0.8381 (tmtm) REVERT: G 20 GLU cc_start: 0.7935 (tt0) cc_final: 0.7376 (tt0) REVERT: E 38 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6213 (tt) REVERT: E 60 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8010 (tmtp) REVERT: C 20 GLU cc_start: 0.7998 (tt0) cc_final: 0.7619 (tt0) REVERT: K 38 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.5499 (tm) REVERT: F 43 LYS cc_start: 0.7325 (tppp) cc_final: 0.7046 (mmmm) REVERT: F 83 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: D 20 GLU cc_start: 0.7881 (tt0) cc_final: 0.7385 (tt0) outliers start: 33 outliers final: 18 residues processed: 86 average time/residue: 0.4070 time to fit residues: 36.1265 Evaluate side-chains 96 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 HIS B 65 ASN F 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.188499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.145516 restraints weight = 3063.275| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.23 r_work: 0.3880 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 3114 Z= 0.250 Angle : 0.654 6.247 4194 Z= 0.384 Chirality : 0.055 0.153 546 Planarity : 0.003 0.016 522 Dihedral : 4.855 16.714 444 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 12.82 % Allowed : 12.18 % Favored : 75.00 % 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 aren not related in a simple way. whole: -3.14 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR L 39 PHE 0.010 0.003 PHE L 94 HIS 0.006 0.003 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 3114) covalent geometry : angle 0.65353 ( 4194) hydrogen bonds : bond 0.03459 ( 56) hydrogen bonds : angle 6.76782 ( 168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 78 time to evaluate : 0.072 Fit side-chains REVERT: L 38 LEU cc_start: 0.6052 (OUTLIER) cc_final: 0.5614 (tm) REVERT: L 58 LYS cc_start: 0.7679 (mttt) cc_final: 0.7477 (mttt) REVERT: L 61 GLU cc_start: 0.8257 (tt0) cc_final: 0.7935 (tp30) REVERT: I 20 GLU cc_start: 0.7735 (tt0) cc_final: 0.7520 (tt0) REVERT: B 38 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5519 (tm) REVERT: B 45 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8067 (ttmt) REVERT: B 60 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8162 (tmtp) REVERT: B 61 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8082 (tp30) REVERT: A 20 GLU cc_start: 0.7918 (tt0) cc_final: 0.7569 (tt0) REVERT: J 60 LYS cc_start: 0.8807 (tttt) cc_final: 0.8391 (tmtm) REVERT: G 20 GLU cc_start: 0.7939 (tt0) cc_final: 0.7410 (tt0) REVERT: E 38 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6397 (tt) REVERT: E 60 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8075 (tmtp) REVERT: C 20 GLU cc_start: 0.8023 (tt0) cc_final: 0.7625 (tt0) REVERT: K 38 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5694 (tm) REVERT: F 43 LYS cc_start: 0.7445 (tppp) cc_final: 0.7136 (mmmm) REVERT: F 83 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8008 (mt-10) outliers start: 40 outliers final: 25 residues processed: 88 average time/residue: 0.4421 time to fit residues: 39.8772 Evaluate side-chains 110 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain D residue 15 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.193706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.151031 restraints weight = 3079.463| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.22 r_work: 0.3954 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3114 Z= 0.132 Angle : 0.524 5.340 4194 Z= 0.305 Chirality : 0.051 0.136 546 Planarity : 0.002 0.010 522 Dihedral : 4.524 17.472 444 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 10.90 % Allowed : 15.71 % Favored : 73.40 % 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 aren not related in a simple way. whole: -2.93 (0.38), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR L 39 PHE 0.011 0.003 PHE F 94 HIS 0.004 0.002 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3114) covalent geometry : angle 0.52395 ( 4194) hydrogen bonds : bond 0.02634 ( 56) hydrogen bonds : angle 6.51189 ( 168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 78 time to evaluate : 0.096 Fit side-chains REVERT: L 38 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5536 (tm) REVERT: I 20 GLU cc_start: 0.7713 (tt0) cc_final: 0.7489 (tt0) REVERT: B 38 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5561 (tm) REVERT: B 60 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8182 (tmtp) REVERT: B 61 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8022 (tp30) REVERT: A 20 GLU cc_start: 0.7910 (tt0) cc_final: 0.7521 (tt0) REVERT: J 38 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.5982 (tt) REVERT: J 60 LYS cc_start: 0.8801 (tttt) cc_final: 0.8415 (tmtm) REVERT: G 20 GLU cc_start: 0.7927 (tt0) cc_final: 0.7363 (tt0) REVERT: E 38 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6393 (tt) REVERT: C 20 GLU cc_start: 0.8019 (tt0) cc_final: 0.7625 (tt0) REVERT: K 38 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5734 (tm) REVERT: F 43 LYS cc_start: 0.7456 (tppp) cc_final: 0.6937 (mmmt) REVERT: F 83 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: D 20 GLU cc_start: 0.7848 (tt0) cc_final: 0.7352 (tt0) outliers start: 34 outliers final: 22 residues processed: 87 average time/residue: 0.4197 time to fit residues: 37.5343 Evaluate side-chains 104 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain D residue 15 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.196487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.154674 restraints weight = 3111.359| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.23 r_work: 0.3933 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3114 Z= 0.156 Angle : 0.546 4.530 4194 Z= 0.321 Chirality : 0.052 0.140 546 Planarity : 0.002 0.014 522 Dihedral : 4.502 16.110 444 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 12.50 % Allowed : 14.10 % Favored : 73.40 % 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 aren not related in a simple way. whole: -2.96 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR L 39 PHE 0.011 0.003 PHE F 94 HIS 0.005 0.002 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3114) covalent geometry : angle 0.54623 ( 4194) hydrogen bonds : bond 0.02718 ( 56) hydrogen bonds : angle 6.50322 ( 168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 74 time to evaluate : 0.126 Fit side-chains REVERT: L 38 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5596 (tm) REVERT: I 20 GLU cc_start: 0.7729 (tt0) cc_final: 0.7503 (tt0) REVERT: B 38 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5601 (tm) REVERT: B 45 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7877 (ttmt) REVERT: B 60 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8145 (tmtp) REVERT: B 61 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: A 20 GLU cc_start: 0.7932 (tt0) cc_final: 0.7564 (tt0) REVERT: J 38 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6121 (tt) REVERT: J 60 LYS cc_start: 0.8797 (tttt) cc_final: 0.8402 (tmtm) REVERT: J 80 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8388 (tttt) REVERT: G 20 GLU cc_start: 0.7961 (tt0) cc_final: 0.7406 (tt0) REVERT: E 38 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6317 (tt) REVERT: C 20 GLU cc_start: 0.8011 (tt0) cc_final: 0.7645 (tt0) REVERT: F 43 LYS cc_start: 0.7471 (tppp) cc_final: 0.6961 (mmmt) REVERT: F 83 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: D 20 GLU cc_start: 0.7870 (tt0) cc_final: 0.7378 (tt0) outliers start: 39 outliers final: 24 residues processed: 88 average time/residue: 0.4301 time to fit residues: 38.9694 Evaluate side-chains 104 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 80 LYS Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain D residue 15 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 36 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN F 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.189563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.146767 restraints weight = 3064.379| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.27 r_work: 0.3894 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3114 Z= 0.221 Angle : 0.648 6.868 4194 Z= 0.379 Chirality : 0.055 0.149 546 Planarity : 0.002 0.014 522 Dihedral : 4.786 17.428 444 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 12.82 % Allowed : 14.42 % Favored : 72.76 % 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 aren not related in a simple way. whole: -3.04 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR L 39 PHE 0.010 0.003 PHE L 94 HIS 0.005 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 3114) covalent geometry : angle 0.64817 ( 4194) hydrogen bonds : bond 0.03154 ( 56) hydrogen bonds : angle 6.67601 ( 168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 78 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: L 38 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5493 (tm) REVERT: L 58 LYS cc_start: 0.7726 (mttt) cc_final: 0.7468 (mttp) REVERT: L 61 GLU cc_start: 0.8225 (tt0) cc_final: 0.7878 (tp30) REVERT: B 38 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5580 (tm) REVERT: B 45 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7725 (ttmt) REVERT: B 61 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8041 (tp30) REVERT: A 20 GLU cc_start: 0.7920 (tt0) cc_final: 0.7489 (tt0) REVERT: J 38 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.5995 (tm) REVERT: J 60 LYS cc_start: 0.8791 (tttt) cc_final: 0.8378 (tmtm) REVERT: G 20 GLU cc_start: 0.7930 (tt0) cc_final: 0.7340 (tt0) REVERT: E 38 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6451 (tt) REVERT: C 20 GLU cc_start: 0.8021 (tt0) cc_final: 0.7621 (tt0) REVERT: F 43 LYS cc_start: 0.7486 (tppp) cc_final: 0.6965 (mmmt) REVERT: F 83 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: D 20 GLU cc_start: 0.7863 (tt0) cc_final: 0.7387 (tt0) outliers start: 40 outliers final: 27 residues processed: 94 average time/residue: 0.4420 time to fit residues: 42.6164 Evaluate side-chains 111 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 80 LYS Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain D residue 15 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.199990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.158555 restraints weight = 3094.386| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.18 r_work: 0.3994 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3114 Z= 0.115 Angle : 0.533 7.590 4194 Z= 0.305 Chirality : 0.051 0.138 546 Planarity : 0.002 0.010 522 Dihedral : 4.414 17.146 444 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 8.97 % Allowed : 18.27 % Favored : 72.76 % 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 aren not related in a simple way. whole: -2.84 (0.38), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR L 39 PHE 0.012 0.003 PHE F 94 HIS 0.003 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3114) covalent geometry : angle 0.53334 ( 4194) hydrogen bonds : bond 0.02419 ( 56) hydrogen bonds : angle 6.34678 ( 168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.078 Fit side-chains REVERT: B 38 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5387 (tm) REVERT: B 61 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7937 (tp30) REVERT: A 20 GLU cc_start: 0.7916 (tt0) cc_final: 0.7570 (tt0) REVERT: J 38 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6093 (tm) REVERT: J 60 LYS cc_start: 0.8781 (tttt) cc_final: 0.8404 (tmtm) REVERT: J 80 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8353 (tttt) REVERT: G 20 GLU cc_start: 0.7925 (tt0) cc_final: 0.7365 (tt0) REVERT: E 38 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6242 (tt) REVERT: E 60 LYS cc_start: 0.8810 (tmtp) cc_final: 0.8193 (tmtm) REVERT: C 20 GLU cc_start: 0.7981 (tt0) cc_final: 0.7607 (tt0) REVERT: F 43 LYS cc_start: 0.7418 (tppp) cc_final: 0.6915 (mmmt) REVERT: D 20 GLU cc_start: 0.7840 (tt0) cc_final: 0.7342 (tt0) outliers start: 28 outliers final: 18 residues processed: 88 average time/residue: 0.3555 time to fit residues: 32.2695 Evaluate side-chains 99 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 80 LYS Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.198653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.156829 restraints weight = 3067.610| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.18 r_work: 0.3968 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3114 Z= 0.132 Angle : 0.565 7.589 4194 Z= 0.324 Chirality : 0.051 0.134 546 Planarity : 0.002 0.010 522 Dihedral : 4.455 18.477 444 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 7.69 % Allowed : 19.87 % Favored : 72.44 % 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 aren not related in a simple way. whole: -2.84 (0.38), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR L 39 PHE 0.011 0.003 PHE F 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3114) covalent geometry : angle 0.56478 ( 4194) hydrogen bonds : bond 0.02518 ( 56) hydrogen bonds : angle 6.28357 ( 168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.118 Fit side-chains REVERT: B 38 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5329 (tm) REVERT: A 20 GLU cc_start: 0.7945 (tt0) cc_final: 0.7575 (tt0) REVERT: J 38 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6081 (tm) REVERT: J 60 LYS cc_start: 0.8807 (tttt) cc_final: 0.8432 (tmtm) REVERT: J 80 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8350 (tttt) REVERT: G 20 GLU cc_start: 0.7902 (tt0) cc_final: 0.7336 (tt0) REVERT: E 38 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6194 (tt) REVERT: E 60 LYS cc_start: 0.8773 (tmtp) cc_final: 0.8214 (tmtm) REVERT: C 20 GLU cc_start: 0.8013 (tt0) cc_final: 0.7622 (tt0) REVERT: F 43 LYS cc_start: 0.7429 (tppp) cc_final: 0.6918 (mmmt) REVERT: D 20 GLU cc_start: 0.7830 (tt0) cc_final: 0.7323 (tt0) outliers start: 24 outliers final: 18 residues processed: 78 average time/residue: 0.3952 time to fit residues: 31.7956 Evaluate side-chains 91 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 80 LYS Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.188087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.143926 restraints weight = 3057.579| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.32 r_work: 0.3852 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 3114 Z= 0.293 Angle : 0.751 6.754 4194 Z= 0.439 Chirality : 0.058 0.158 546 Planarity : 0.003 0.015 522 Dihedral : 5.067 18.836 444 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 9.62 % Allowed : 17.95 % Favored : 72.44 % 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 aren not related in a simple way. whole: -3.05 (0.37), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR E 39 PHE 0.011 0.003 PHE L 94 HIS 0.006 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00652 ( 3114) covalent geometry : angle 0.75081 ( 4194) hydrogen bonds : bond 0.03578 ( 56) hydrogen bonds : angle 6.67521 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1317.35 seconds wall clock time: 23 minutes 7.42 seconds (1387.42 seconds total)