Starting phenix.real_space_refine on Tue Mar 3 11:06:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wap_65826/03_2026/9wap_65826.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wap_65826/03_2026/9wap_65826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wap_65826/03_2026/9wap_65826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wap_65826/03_2026/9wap_65826.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wap_65826/03_2026/9wap_65826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wap_65826/03_2026/9wap_65826.map" } resolution = 3.22 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1764 2.51 5 N 468 2.21 5 O 468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2712 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 0.32, per 1000 atoms: 0.12 Number of scatterers: 2712 At special positions: 0 Unit cell: (56.852, 84.812, 45.668, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 468 8.00 N 468 7.00 C 1764 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: 0.11 Conformation dependent library (CDL) restraints added in 102.6 milliseconds 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 38.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 18 through 20 removed outlier: 6.445A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL C 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL I 18 " --> pdb=" O PHE K 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 24 through 27 removed outlier: 6.917A pdb=" N GLY E 25 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ASN G 27 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER A 26 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N VAL A 24 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASN C 27 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N SER A 26 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N VAL C 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASN I 27 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N SER C 26 " --> pdb=" O ASN I 27 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY I 25 " --> pdb=" O VAL K 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 30 through 36 removed outlier: 7.014A pdb=" N LEU G 34 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N MET E 35 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL G 36 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU A 34 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N MET G 35 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 36 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE A 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU C 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLY A 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 10.489A pdb=" N VAL C 36 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N MET A 35 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE C 31 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU I 34 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLY C 33 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N VAL I 36 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N MET C 35 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU K 34 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N MET I 35 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL K 36 " --> pdb=" O MET I 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 39 through 40 removed outlier: 6.307A pdb=" N VAL E 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL C 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL I 39 " --> pdb=" O VAL K 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 18 through 20 removed outlier: 6.476A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL J 18 " --> pdb=" O PHE L 19 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.935A pdb=" N GLY F 25 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 24 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ASN H 27 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N SER B 26 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N VAL B 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASN D 27 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N SER B 26 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N VAL D 24 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASN J 27 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N SER D 26 " --> pdb=" O ASN J 27 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N VAL J 24 " --> pdb=" O GLY L 25 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ASN L 27 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N SER J 26 " --> pdb=" O ASN L 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 30 through 36 removed outlier: 6.101A pdb=" N ILE F 31 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU H 34 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLY F 33 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL H 36 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N MET F 35 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 30 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N GLY H 33 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N ILE B 32 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N MET H 35 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N LEU B 34 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE B 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU D 34 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLY B 33 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 10.491A pdb=" N VAL D 36 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N MET B 35 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE D 31 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU J 34 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLY D 33 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 10.480A pdb=" N VAL J 36 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N MET D 35 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU L 34 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N MET J 35 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL L 36 " --> pdb=" O MET J 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 39 through 40 removed outlier: 6.330A pdb=" N VAL F 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL D 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL J 39 " --> pdb=" O VAL L 40 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 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: 0.23 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 888 1.34 - 1.46: 405 1.46 - 1.57: 1431 1.57 - 1.68: 0 1.68 - 1.80: 24 Bond restraints: 2748 Sorted by residual: bond pdb=" CB VAL B 24 " pdb=" CG1 VAL B 24 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.39e+00 bond pdb=" CB VAL K 24 " pdb=" CG1 VAL K 24 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.38e+00 bond pdb=" CB VAL L 24 " pdb=" CG1 VAL L 24 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.34e+00 bond pdb=" CB VAL D 24 " pdb=" CG1 VAL D 24 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.34e+00 bond pdb=" CB VAL G 24 " pdb=" CG1 VAL G 24 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.32e+00 ... (remaining 2743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 3504 1.01 - 2.01: 132 2.01 - 3.02: 24 3.02 - 4.03: 24 4.03 - 5.03: 12 Bond angle restraints: 3696 Sorted by residual: angle pdb=" CG1 VAL F 24 " pdb=" CB VAL F 24 " pdb=" CG2 VAL F 24 " ideal model delta sigma weight residual 110.80 105.77 5.03 2.20e+00 2.07e-01 5.23e+00 angle pdb=" CG1 VAL K 24 " pdb=" CB VAL K 24 " pdb=" CG2 VAL K 24 " ideal model delta sigma weight residual 110.80 105.77 5.03 2.20e+00 2.07e-01 5.23e+00 angle pdb=" CG1 VAL B 24 " pdb=" CB VAL B 24 " pdb=" CG2 VAL B 24 " ideal model delta sigma weight residual 110.80 105.77 5.03 2.20e+00 2.07e-01 5.22e+00 angle pdb=" CG1 VAL E 24 " pdb=" CB VAL E 24 " pdb=" CG2 VAL E 24 " ideal model delta sigma weight residual 110.80 105.78 5.02 2.20e+00 2.07e-01 5.21e+00 angle pdb=" CG1 VAL J 24 " pdb=" CB VAL J 24 " pdb=" CG2 VAL J 24 " ideal model delta sigma weight residual 110.80 105.78 5.02 2.20e+00 2.07e-01 5.21e+00 ... (remaining 3691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.11: 1320 10.11 - 20.22: 108 20.22 - 30.33: 72 30.33 - 40.44: 24 40.44 - 50.55: 24 Dihedral angle restraints: 1548 sinusoidal: 564 harmonic: 984 Sorted by residual: dihedral pdb=" CA GLU L 22 " pdb=" C GLU L 22 " pdb=" N ASP L 23 " pdb=" CA ASP L 23 " ideal model delta harmonic sigma weight residual -180.00 -167.48 -12.52 0 5.00e+00 4.00e-02 6.27e+00 dihedral pdb=" CA GLU K 22 " pdb=" C GLU K 22 " pdb=" N ASP K 23 " pdb=" CA ASP K 23 " ideal model delta harmonic sigma weight residual -180.00 -167.49 -12.51 0 5.00e+00 4.00e-02 6.26e+00 dihedral pdb=" CA GLU B 22 " pdb=" C GLU B 22 " pdb=" N ASP B 23 " pdb=" CA ASP B 23 " ideal model delta harmonic sigma weight residual 180.00 -167.49 -12.51 0 5.00e+00 4.00e-02 6.26e+00 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 191 0.026 - 0.052: 112 0.052 - 0.077: 45 0.077 - 0.103: 46 0.103 - 0.129: 50 Chirality restraints: 444 Sorted by residual: chirality pdb=" CA ILE E 31 " pdb=" N ILE E 31 " pdb=" C ILE E 31 " pdb=" CB ILE E 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE F 31 " pdb=" N ILE F 31 " pdb=" C ILE F 31 " pdb=" CB ILE F 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 441 not shown) Planarity restraints: 468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL J 24 " -0.004 2.00e-02 2.50e+03 7.40e-03 5.48e-01 pdb=" C VAL J 24 " 0.013 2.00e-02 2.50e+03 pdb=" O VAL J 24 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY J 25 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 24 " -0.004 2.00e-02 2.50e+03 7.35e-03 5.40e-01 pdb=" C VAL F 24 " 0.013 2.00e-02 2.50e+03 pdb=" O VAL F 24 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY F 25 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 24 " -0.004 2.00e-02 2.50e+03 7.28e-03 5.29e-01 pdb=" C VAL B 24 " 0.013 2.00e-02 2.50e+03 pdb=" O VAL B 24 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY B 25 " -0.004 2.00e-02 2.50e+03 ... (remaining 465 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 1705 3.05 - 3.51: 2702 3.51 - 3.97: 4101 3.97 - 4.44: 4971 4.44 - 4.90: 9049 Nonbonded interactions: 22528 Sorted by model distance: nonbonded pdb=" O ASN C 27 " pdb=" N GLY I 29 " model vdw 2.587 3.120 nonbonded pdb=" O ASN B 27 " pdb=" N GLY D 29 " model vdw 2.638 3.120 nonbonded pdb=" N ILE G 41 " pdb=" N ALA G 42 " model vdw 2.645 2.560 nonbonded pdb=" N ILE L 41 " pdb=" N ALA L 42 " model vdw 2.645 2.560 nonbonded pdb=" N ILE K 41 " pdb=" N ALA K 42 " model vdw 2.645 2.560 ... (remaining 22523 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.200 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.950 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.006 0.061 2748 Z= 0.203 Angle : 0.643 5.033 3696 Z= 0.339 Chirality : 0.057 0.129 444 Planarity : 0.002 0.007 468 Dihedral : 13.598 50.555 924 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.47), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.29 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE H 19 HIS 0.002 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 2748) covalent geometry : angle 0.64290 ( 3696) hydrogen bonds : bond 0.15332 ( 24) hydrogen bonds : angle 8.34614 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.078 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0288 time to fit residues: 2.8204 Evaluate side-chains 61 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN D 15 GLN ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.120364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.095401 restraints weight = 3121.239| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.51 r_work: 0.3223 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2748 Z= 0.217 Angle : 0.570 6.986 3696 Z= 0.300 Chirality : 0.058 0.171 444 Planarity : 0.002 0.009 468 Dihedral : 5.646 15.805 372 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 6.16 % Allowed : 16.30 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.46), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.14 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE K 19 HIS 0.001 0.000 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 2748) covalent geometry : angle 0.56999 ( 3696) hydrogen bonds : bond 0.01406 ( 24) hydrogen bonds : angle 5.98036 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.067 Fit side-chains REVERT: I 15 GLN cc_start: 0.8503 (tt0) cc_final: 0.7972 (tm-30) REVERT: J 15 GLN cc_start: 0.8485 (tt0) cc_final: 0.7945 (tm-30) outliers start: 17 outliers final: 16 residues processed: 65 average time/residue: 0.0364 time to fit residues: 3.0792 Evaluate side-chains 75 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 35 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 15 GLN C 15 GLN D 15 GLN ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.131000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.107349 restraints weight = 3097.853| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.47 r_work: 0.3212 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2748 Z= 0.221 Angle : 0.594 6.978 3696 Z= 0.309 Chirality : 0.059 0.165 444 Planarity : 0.002 0.009 468 Dihedral : 5.503 15.058 372 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 10.51 % Allowed : 15.58 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.45), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.03 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE I 19 HIS 0.001 0.000 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 2748) covalent geometry : angle 0.59371 ( 3696) hydrogen bonds : bond 0.01364 ( 24) hydrogen bonds : angle 5.71925 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.078 Fit side-chains REVERT: E 22 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: F 22 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: I 15 GLN cc_start: 0.8581 (tt0) cc_final: 0.7944 (tm-30) REVERT: J 15 GLN cc_start: 0.8555 (tt0) cc_final: 0.7910 (tm-30) outliers start: 29 outliers final: 22 residues processed: 72 average time/residue: 0.0374 time to fit residues: 3.5476 Evaluate side-chains 84 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 35 MET Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 35 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 17 optimal weight: 5.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 15 GLN C 15 GLN D 15 GLN I 13 HIS ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.117930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.093286 restraints weight = 3063.179| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.50 r_work: 0.3190 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2748 Z= 0.224 Angle : 0.636 7.564 3696 Z= 0.325 Chirality : 0.061 0.183 444 Planarity : 0.002 0.009 468 Dihedral : 5.517 14.558 372 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 10.87 % Allowed : 13.41 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.45), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.19 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE K 19 HIS 0.002 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 2748) covalent geometry : angle 0.63565 ( 3696) hydrogen bonds : bond 0.01219 ( 24) hydrogen bonds : angle 5.39878 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.076 Fit side-chains REVERT: B 35 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7783 (ptt) REVERT: E 22 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: F 22 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: I 15 GLN cc_start: 0.8634 (tt0) cc_final: 0.7902 (tm-30) REVERT: J 15 GLN cc_start: 0.8614 (tt0) cc_final: 0.7878 (tm-30) outliers start: 30 outliers final: 25 residues processed: 66 average time/residue: 0.0357 time to fit residues: 3.0763 Evaluate side-chains 80 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 52 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 35 MET Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 35 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 14 optimal weight: 0.0270 chunk 35 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 15 GLN B 13 HIS B 15 GLN C 15 GLN D 15 GLN J 13 HIS K 14 HIS K 15 GLN L 14 HIS L 15 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.112218 restraints weight = 2941.627| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.60 r_work: 0.3331 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2748 Z= 0.137 Angle : 0.612 8.594 3696 Z= 0.309 Chirality : 0.061 0.197 444 Planarity : 0.002 0.009 468 Dihedral : 5.273 14.699 372 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 8.70 % Allowed : 16.67 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.26 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE K 19 HIS 0.001 0.000 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2748) covalent geometry : angle 0.61190 ( 3696) hydrogen bonds : bond 0.00955 ( 24) hydrogen bonds : angle 5.09001 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.073 Fit side-chains REVERT: A 15 GLN cc_start: 0.8316 (tt0) cc_final: 0.7531 (tm-30) REVERT: B 15 GLN cc_start: 0.8182 (tt0) cc_final: 0.7377 (tm-30) REVERT: I 15 GLN cc_start: 0.8527 (tt0) cc_final: 0.7857 (tm-30) REVERT: J 15 GLN cc_start: 0.8517 (tt0) cc_final: 0.7835 (tm-30) REVERT: K 35 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7748 (ptt) outliers start: 24 outliers final: 22 residues processed: 66 average time/residue: 0.0363 time to fit residues: 3.1295 Evaluate side-chains 76 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 35 MET Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 35 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN D 15 GLN K 15 GLN L 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.124579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.099918 restraints weight = 3074.117| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.52 r_work: 0.3200 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.033 2748 Z= 0.344 Angle : 0.700 7.847 3696 Z= 0.364 Chirality : 0.061 0.160 444 Planarity : 0.003 0.012 468 Dihedral : 5.963 15.950 372 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 11.23 % Allowed : 14.49 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.42 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE K 19 HIS 0.003 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00837 ( 2748) covalent geometry : angle 0.69966 ( 3696) hydrogen bonds : bond 0.01504 ( 24) hydrogen bonds : angle 5.47985 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.107 Fit side-chains REVERT: B 35 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7834 (ptt) REVERT: E 22 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: F 22 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: G 22 GLU cc_start: 0.8577 (tt0) cc_final: 0.8325 (tt0) REVERT: H 22 GLU cc_start: 0.8598 (tt0) cc_final: 0.8348 (tt0) REVERT: I 15 GLN cc_start: 0.8566 (tt0) cc_final: 0.8148 (tt0) REVERT: J 15 GLN cc_start: 0.8590 (tt0) cc_final: 0.8184 (tt0) outliers start: 31 outliers final: 26 residues processed: 78 average time/residue: 0.0487 time to fit residues: 4.7498 Evaluate side-chains 88 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 35 MET Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 35 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN K 15 GLN L 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.129420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.104374 restraints weight = 2982.215| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.47 r_work: 0.3292 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2748 Z= 0.197 Angle : 0.653 8.767 3696 Z= 0.332 Chirality : 0.061 0.206 444 Planarity : 0.002 0.010 468 Dihedral : 5.620 19.395 372 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 11.23 % Allowed : 14.86 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.43 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE L 19 HIS 0.001 0.000 HIS G 13 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 2748) covalent geometry : angle 0.65283 ( 3696) hydrogen bonds : bond 0.01145 ( 24) hydrogen bonds : angle 5.20721 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.067 Fit side-chains REVERT: B 35 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7723 (ptt) REVERT: I 15 GLN cc_start: 0.8515 (tt0) cc_final: 0.7734 (tm-30) REVERT: J 15 GLN cc_start: 0.8522 (tt0) cc_final: 0.7727 (tm-30) outliers start: 31 outliers final: 25 residues processed: 77 average time/residue: 0.0397 time to fit residues: 3.9590 Evaluate side-chains 88 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 35 MET Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 35 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN K 15 GLN L 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.127086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.101814 restraints weight = 3088.392| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.59 r_work: 0.3245 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2748 Z= 0.246 Angle : 0.707 9.359 3696 Z= 0.358 Chirality : 0.062 0.220 444 Planarity : 0.002 0.010 468 Dihedral : 5.875 17.805 372 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 9.78 % Allowed : 17.03 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.53 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE L 19 HIS 0.002 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 2748) covalent geometry : angle 0.70711 ( 3696) hydrogen bonds : bond 0.01278 ( 24) hydrogen bonds : angle 5.24928 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.098 Fit side-chains REVERT: B 35 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7772 (ptt) outliers start: 27 outliers final: 26 residues processed: 76 average time/residue: 0.0467 time to fit residues: 4.5326 Evaluate side-chains 88 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 35 MET Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 35 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN I 15 GLN J 15 GLN K 15 GLN L 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.129577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.104179 restraints weight = 3098.638| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.63 r_work: 0.3276 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2748 Z= 0.238 Angle : 0.727 8.949 3696 Z= 0.367 Chirality : 0.062 0.210 444 Planarity : 0.002 0.009 468 Dihedral : 5.881 18.293 372 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 10.14 % Allowed : 18.48 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.55 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE L 19 HIS 0.002 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00569 ( 2748) covalent geometry : angle 0.72727 ( 3696) hydrogen bonds : bond 0.01232 ( 24) hydrogen bonds : angle 5.25799 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.102 Fit side-chains REVERT: B 35 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7727 (ptt) REVERT: I 15 GLN cc_start: 0.8385 (tt0) cc_final: 0.7874 (tm-30) REVERT: J 15 GLN cc_start: 0.8379 (tt0) cc_final: 0.7856 (tm-30) outliers start: 28 outliers final: 26 residues processed: 72 average time/residue: 0.0459 time to fit residues: 4.2093 Evaluate side-chains 85 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 35 MET Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 35 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 0.0010 chunk 10 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 overall best weight: 2.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 15 GLN K 15 GLN L 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.132707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.107367 restraints weight = 3023.683| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.55 r_work: 0.3311 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2748 Z= 0.153 Angle : 0.684 8.513 3696 Z= 0.346 Chirality : 0.062 0.216 444 Planarity : 0.002 0.009 468 Dihedral : 5.681 21.844 372 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 8.33 % Allowed : 19.93 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.56 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE K 19 HIS 0.001 0.000 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 2748) covalent geometry : angle 0.68412 ( 3696) hydrogen bonds : bond 0.00995 ( 24) hydrogen bonds : angle 5.03793 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.081 Fit side-chains REVERT: A 15 GLN cc_start: 0.8292 (tt0) cc_final: 0.7455 (tm-30) REVERT: B 15 GLN cc_start: 0.8196 (tt0) cc_final: 0.7353 (tm-30) REVERT: B 35 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7722 (ptt) REVERT: I 15 GLN cc_start: 0.8348 (tt0) cc_final: 0.7758 (tm-30) REVERT: J 15 GLN cc_start: 0.8354 (tt0) cc_final: 0.7745 (tm-30) REVERT: K 35 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7904 (ptt) outliers start: 23 outliers final: 21 residues processed: 69 average time/residue: 0.0471 time to fit residues: 4.1347 Evaluate side-chains 82 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 35 MET Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 35 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 31 optimal weight: 0.0570 chunk 10 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 15 GLN L 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.133925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.108629 restraints weight = 3013.392| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.55 r_work: 0.3323 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2748 Z= 0.143 Angle : 0.688 8.270 3696 Z= 0.348 Chirality : 0.062 0.208 444 Planarity : 0.002 0.009 468 Dihedral : 5.626 23.453 372 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 8.33 % Allowed : 20.29 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.43), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.56 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE I 19 HIS 0.001 0.000 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 2748) covalent geometry : angle 0.68783 ( 3696) hydrogen bonds : bond 0.00928 ( 24) hydrogen bonds : angle 4.96947 ( 72) =============================================================================== Job complete usr+sys time: 710.77 seconds wall clock time: 12 minutes 47.57 seconds (767.57 seconds total)