Starting phenix.real_space_refine on Fri Aug 22 15:03:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aex_15388/08_2025/8aex_15388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aex_15388/08_2025/8aex_15388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8aex_15388/08_2025/8aex_15388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aex_15388/08_2025/8aex_15388.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8aex_15388/08_2025/8aex_15388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aex_15388/08_2025/8aex_15388.map" } resolution = 2.76 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= 0.001 sd= 0.011 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 2925 2.51 5 N 810 2.21 5 O 930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 4665 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 483 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain breaks: 1 Chain: "B" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 450 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Restraints were copied for chains: C, E, G, I, D, F, H, J Time building chain proxies: 0.88, per 1000 atoms: 0.19 Number of scatterers: 4665 At special positions: 0 Unit cell: (109.2, 94.5, 49.35, 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 930 8.00 N 810 7.00 C 2925 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: 0.31 Conformation dependent library (CDL) restraints added in 178.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 47.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 44 removed outlier: 6.694A pdb=" N GLY A 36 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY C 36 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY E 36 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY G 36 " --> pdb=" O GLU I 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 6.526A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL E 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLY C 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N THR E 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ALA C 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 49 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL G 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLY E 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 10.097A pdb=" N THR G 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ALA E 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL G 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL I 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLY G 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 10.097A pdb=" N THR I 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N ALA G 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.319A pdb=" N VAL A 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL C 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL E 77 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL G 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 88 through 96 Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 43 Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 57 removed outlier: 6.847A pdb=" N GLY B 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL D 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS D 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY B 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY D 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL F 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL D 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS F 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY D 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY F 47 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL H 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL F 49 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS H 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY F 51 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY H 47 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL J 48 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL H 49 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS J 50 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY H 51 " --> pdb=" O HIS J 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 67 removed outlier: 6.371A pdb=" N VAL B 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL D 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASN B 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL D 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL F 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN D 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL F 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL H 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN F 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL H 63 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL J 66 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN H 65 " --> pdb=" O VAL J 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 70 through 72 Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 79 Processing sheet with id=AB3, first strand: chain 'B' and resid 88 through 94 180 hydrogen bonds defined for protein. 540 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: 0.64 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.25: 810 1.25 - 1.33: 514 1.33 - 1.41: 366 1.41 - 1.48: 790 1.48 - 1.56: 2200 Bond restraints: 4680 Sorted by residual: bond pdb=" C LYS E 60 " pdb=" O LYS E 60 " ideal model delta sigma weight residual 1.234 1.196 0.039 8.30e-03 1.45e+04 2.17e+01 bond pdb=" C LYS A 60 " pdb=" O LYS A 60 " ideal model delta sigma weight residual 1.234 1.196 0.039 8.30e-03 1.45e+04 2.16e+01 bond pdb=" C LYS I 60 " pdb=" O LYS I 60 " ideal model delta sigma weight residual 1.234 1.196 0.039 8.30e-03 1.45e+04 2.16e+01 bond pdb=" C LYS C 60 " pdb=" O LYS C 60 " ideal model delta sigma weight residual 1.234 1.196 0.038 8.30e-03 1.45e+04 2.15e+01 bond pdb=" C LYS G 60 " pdb=" O LYS G 60 " ideal model delta sigma weight residual 1.234 1.196 0.038 8.30e-03 1.45e+04 2.14e+01 ... (remaining 4675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 5884 2.12 - 4.24: 341 4.24 - 6.36: 70 6.36 - 8.48: 15 8.48 - 10.60: 5 Bond angle restraints: 6315 Sorted by residual: angle pdb=" N ALA B 90 " pdb=" CA ALA B 90 " pdb=" C ALA B 90 " ideal model delta sigma weight residual 109.52 117.52 -8.00 1.55e+00 4.16e-01 2.66e+01 angle pdb=" N ALA H 90 " pdb=" CA ALA H 90 " pdb=" C ALA H 90 " ideal model delta sigma weight residual 109.52 117.51 -7.99 1.55e+00 4.16e-01 2.66e+01 angle pdb=" N ALA F 90 " pdb=" CA ALA F 90 " pdb=" C ALA F 90 " ideal model delta sigma weight residual 109.52 117.50 -7.98 1.55e+00 4.16e-01 2.65e+01 angle pdb=" N ALA D 90 " pdb=" CA ALA D 90 " pdb=" C ALA D 90 " ideal model delta sigma weight residual 109.52 117.50 -7.98 1.55e+00 4.16e-01 2.65e+01 angle pdb=" N ALA J 90 " pdb=" CA ALA J 90 " pdb=" C ALA J 90 " ideal model delta sigma weight residual 109.52 117.50 -7.98 1.55e+00 4.16e-01 2.65e+01 ... (remaining 6310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.02: 2365 14.02 - 28.03: 210 28.03 - 42.04: 100 42.04 - 56.06: 35 56.06 - 70.07: 25 Dihedral angle restraints: 2735 sinusoidal: 910 harmonic: 1825 Sorted by residual: dihedral pdb=" CA VAL E 82 " pdb=" C VAL E 82 " pdb=" N GLU E 83 " pdb=" CA GLU E 83 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA VAL I 82 " pdb=" C VAL I 82 " pdb=" N GLU I 83 " pdb=" CA GLU I 83 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA VAL C 82 " pdb=" C VAL C 82 " pdb=" N GLU C 83 " pdb=" CA GLU C 83 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 2732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 487 0.051 - 0.101: 253 0.101 - 0.152: 90 0.152 - 0.202: 0 0.202 - 0.253: 5 Chirality restraints: 835 Sorted by residual: chirality pdb=" CA GLU J 35 " pdb=" N GLU J 35 " pdb=" C GLU J 35 " pdb=" CB GLU J 35 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA GLU H 35 " pdb=" N GLU H 35 " pdb=" C GLU H 35 " pdb=" CB GLU H 35 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA GLU F 35 " pdb=" N GLU F 35 " pdb=" C GLU F 35 " pdb=" CB GLU F 35 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 832 not shown) Planarity restraints: 775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 60 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C LYS F 60 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS F 60 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU F 61 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 60 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C LYS D 60 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS D 60 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU D 61 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS J 60 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C LYS J 60 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS J 60 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU J 61 " 0.013 2.00e-02 2.50e+03 ... (remaining 772 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1414 2.83 - 3.35: 3724 3.35 - 3.87: 8513 3.87 - 4.38: 9482 4.38 - 4.90: 17976 Nonbonded interactions: 41109 Sorted by model distance: nonbonded pdb=" O GLU A 83 " pdb=" OE1 GLU A 83 " model vdw 2.313 3.040 nonbonded pdb=" O GLU C 83 " pdb=" OE1 GLU C 83 " model vdw 2.313 3.040 nonbonded pdb=" O GLU I 83 " pdb=" OE1 GLU I 83 " model vdw 2.313 3.040 nonbonded pdb=" O GLU G 83 " pdb=" OE1 GLU G 83 " model vdw 2.313 3.040 nonbonded pdb=" O GLU E 83 " pdb=" OE1 GLU E 83 " model vdw 2.313 3.040 ... (remaining 41104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 5.650 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.009 0.059 4680 Z= 0.625 Angle : 1.159 10.601 6315 Z= 0.728 Chirality : 0.064 0.253 835 Planarity : 0.005 0.022 775 Dihedral : 16.568 70.074 1585 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.19 % Allowed : 19.15 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.01 (0.28), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.21), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.004 TYR D 39 PHE 0.012 0.003 PHE A 94 HIS 0.004 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00891 ( 4680) covalent geometry : angle 1.15908 ( 6315) hydrogen bonds : bond 0.13633 ( 180) hydrogen bonds : angle 7.79266 ( 540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.180 Fit side-chains REVERT: A 45 LYS cc_start: 0.8522 (tttp) cc_final: 0.8303 (tttp) REVERT: A 58 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8314 (mttp) REVERT: B 58 LYS cc_start: 0.8779 (mttm) cc_final: 0.8391 (mttm) REVERT: C 45 LYS cc_start: 0.8492 (tttp) cc_final: 0.8284 (tttp) REVERT: C 58 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8385 (mttm) REVERT: D 58 LYS cc_start: 0.8589 (mttm) cc_final: 0.8231 (mttp) REVERT: E 45 LYS cc_start: 0.8442 (tttp) cc_final: 0.8239 (tttp) REVERT: H 44 THR cc_start: 0.8967 (t) cc_final: 0.8657 (m) REVERT: H 58 LYS cc_start: 0.8652 (mttm) cc_final: 0.8282 (mttp) REVERT: I 34 LYS cc_start: 0.8387 (mttt) cc_final: 0.8173 (mtmt) REVERT: I 58 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8294 (mttp) REVERT: J 35 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6545 (tm-30) outliers start: 15 outliers final: 5 residues processed: 111 average time/residue: 0.6075 time to fit residues: 69.4607 Evaluate side-chains 105 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 44 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN H 65 ASN J 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.110837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.095990 restraints weight = 6233.235| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.91 r_work: 0.3414 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4680 Z= 0.159 Angle : 0.603 5.391 6315 Z= 0.343 Chirality : 0.053 0.128 835 Planarity : 0.003 0.011 775 Dihedral : 5.776 22.171 680 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.83 % Allowed : 20.43 % Favored : 75.74 % 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 aren not related in a simple way. whole: -2.52 (0.30), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR I 39 PHE 0.018 0.004 PHE D 94 HIS 0.002 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4680) covalent geometry : angle 0.60286 ( 6315) hydrogen bonds : bond 0.03270 ( 180) hydrogen bonds : angle 5.62658 ( 540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.143 Fit side-chains REVERT: B 58 LYS cc_start: 0.8991 (mttm) cc_final: 0.8587 (mttm) REVERT: D 58 LYS cc_start: 0.8829 (mttm) cc_final: 0.8411 (mttp) REVERT: F 35 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6978 (tm-30) REVERT: H 83 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7178 (tp30) REVERT: I 58 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8360 (mttp) REVERT: J 35 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6771 (tm-30) outliers start: 18 outliers final: 10 residues processed: 104 average time/residue: 0.6137 time to fit residues: 65.7340 Evaluate side-chains 98 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 51 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 0.0050 chunk 58 optimal weight: 5.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 65 ASN I 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.107600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.092575 restraints weight = 6250.433| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.91 r_work: 0.3366 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 4680 Z= 0.244 Angle : 0.640 5.796 6315 Z= 0.358 Chirality : 0.054 0.132 835 Planarity : 0.003 0.014 775 Dihedral : 5.864 23.743 679 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 5.11 % Allowed : 20.00 % Favored : 74.89 % 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: -2.44 (0.30), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR F 39 PHE 0.019 0.004 PHE G 94 HIS 0.004 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 4680) covalent geometry : angle 0.64029 ( 6315) hydrogen bonds : bond 0.03237 ( 180) hydrogen bonds : angle 5.28258 ( 540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.140 Fit side-chains REVERT: A 58 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8172 (mttp) REVERT: B 58 LYS cc_start: 0.8996 (mttm) cc_final: 0.8669 (mttp) REVERT: C 58 LYS cc_start: 0.8754 (mtpt) cc_final: 0.8407 (mttm) REVERT: D 58 LYS cc_start: 0.8793 (mttm) cc_final: 0.8575 (mttm) REVERT: F 35 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6970 (tm-30) REVERT: H 46 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: I 58 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8244 (mttp) REVERT: J 35 GLU cc_start: 0.7377 (tm-30) cc_final: 0.6807 (tm-30) outliers start: 24 outliers final: 11 residues processed: 108 average time/residue: 0.6659 time to fit residues: 73.9207 Evaluate side-chains 103 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN H 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.106316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.091284 restraints weight = 6245.038| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.91 r_work: 0.3344 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 4680 Z= 0.305 Angle : 0.678 5.912 6315 Z= 0.379 Chirality : 0.055 0.139 835 Planarity : 0.003 0.015 775 Dihedral : 6.112 25.720 679 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 6.38 % Allowed : 20.21 % 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: -2.48 (0.30), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR J 39 PHE 0.020 0.005 PHE G 94 HIS 0.005 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 4680) covalent geometry : angle 0.67823 ( 6315) hydrogen bonds : bond 0.03186 ( 180) hydrogen bonds : angle 5.26241 ( 540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.139 Fit side-chains REVERT: A 58 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8128 (mttp) REVERT: A 62 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8285 (tm-30) REVERT: B 45 LYS cc_start: 0.8476 (mmtp) cc_final: 0.8223 (mttp) REVERT: B 58 LYS cc_start: 0.9045 (mttm) cc_final: 0.8702 (mttm) REVERT: C 58 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8361 (mttm) REVERT: D 83 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7311 (tp30) REVERT: F 35 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7064 (tm-30) REVERT: F 58 LYS cc_start: 0.8977 (mttm) cc_final: 0.8631 (mttm) REVERT: G 57 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: H 46 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: H 83 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7171 (tp30) REVERT: I 58 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8222 (mttp) REVERT: J 35 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6818 (tm-30) REVERT: J 96 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7820 (mtpp) outliers start: 30 outliers final: 17 residues processed: 114 average time/residue: 0.6494 time to fit residues: 76.2758 Evaluate side-chains 110 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.106511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.091506 restraints weight = 6271.868| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.92 r_work: 0.3348 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 4680 Z= 0.286 Angle : 0.670 5.652 6315 Z= 0.373 Chirality : 0.055 0.134 835 Planarity : 0.003 0.010 775 Dihedral : 6.164 25.291 679 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 7.02 % Allowed : 19.36 % Favored : 73.62 % 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: -2.53 (0.29), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR F 39 PHE 0.020 0.004 PHE G 94 HIS 0.004 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 4680) covalent geometry : angle 0.67049 ( 6315) hydrogen bonds : bond 0.03057 ( 180) hydrogen bonds : angle 5.20613 ( 540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.186 Fit side-chains REVERT: A 58 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8217 (mttp) REVERT: A 62 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: B 58 LYS cc_start: 0.9063 (mttm) cc_final: 0.8710 (mttm) REVERT: B 83 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7652 (tp30) REVERT: C 58 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8450 (mttm) REVERT: D 83 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7179 (tp30) REVERT: F 35 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7118 (tm-30) REVERT: F 58 LYS cc_start: 0.9003 (mttm) cc_final: 0.8786 (mttm) REVERT: F 83 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7522 (tm-30) REVERT: G 57 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: H 83 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7246 (tp30) REVERT: I 58 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8194 (mttp) REVERT: J 35 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6820 (tm-30) REVERT: J 45 LYS cc_start: 0.8576 (mmtp) cc_final: 0.8249 (mttp) REVERT: J 96 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7790 (mtpp) outliers start: 33 outliers final: 21 residues processed: 115 average time/residue: 0.6137 time to fit residues: 72.8022 Evaluate side-chains 114 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN H 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.108337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.093506 restraints weight = 6265.194| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.92 r_work: 0.3386 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4680 Z= 0.212 Angle : 0.622 5.745 6315 Z= 0.346 Chirality : 0.053 0.134 835 Planarity : 0.002 0.018 775 Dihedral : 5.963 24.849 679 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 6.38 % Allowed : 20.43 % 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 aren not related in a simple way. whole: -2.51 (0.29), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR J 39 PHE 0.018 0.004 PHE G 94 HIS 0.003 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 4680) covalent geometry : angle 0.62157 ( 6315) hydrogen bonds : bond 0.02789 ( 180) hydrogen bonds : angle 5.08805 ( 540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.184 Fit side-chains REVERT: A 58 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8170 (mttp) REVERT: B 58 LYS cc_start: 0.9058 (mttm) cc_final: 0.8683 (mttm) REVERT: C 58 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8466 (mttm) REVERT: D 83 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7315 (tp30) REVERT: F 35 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7107 (tm-30) REVERT: G 44 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8572 (m) REVERT: G 57 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: H 46 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: H 58 LYS cc_start: 0.9048 (mttm) cc_final: 0.8777 (mttp) REVERT: H 83 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7283 (tp30) REVERT: I 58 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8232 (mttp) REVERT: J 35 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6812 (tm-30) REVERT: J 45 LYS cc_start: 0.8566 (mmtp) cc_final: 0.8233 (mttp) REVERT: J 96 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7762 (mtpp) outliers start: 30 outliers final: 18 residues processed: 114 average time/residue: 0.5922 time to fit residues: 69.6675 Evaluate side-chains 112 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.106973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.092040 restraints weight = 6212.592| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.91 r_work: 0.3368 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4680 Z= 0.266 Angle : 0.669 6.494 6315 Z= 0.371 Chirality : 0.054 0.145 835 Planarity : 0.003 0.021 775 Dihedral : 6.091 25.779 679 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 7.23 % Allowed : 21.28 % Favored : 71.49 % 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: -2.52 (0.29), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR F 39 PHE 0.020 0.004 PHE G 94 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 4680) covalent geometry : angle 0.66876 ( 6315) hydrogen bonds : bond 0.02944 ( 180) hydrogen bonds : angle 5.05064 ( 540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.135 Fit side-chains REVERT: A 58 LYS cc_start: 0.8725 (mtpt) cc_final: 0.8193 (mttp) REVERT: A 62 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: B 58 LYS cc_start: 0.9085 (mttm) cc_final: 0.8830 (mttm) REVERT: C 58 LYS cc_start: 0.8665 (mtpt) cc_final: 0.8426 (mttm) REVERT: D 83 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7266 (tp30) REVERT: F 35 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7148 (tm-30) REVERT: G 57 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: H 46 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: H 83 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7319 (tp30) REVERT: I 58 LYS cc_start: 0.8826 (mtpt) cc_final: 0.8261 (mttp) REVERT: J 35 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6832 (tm-30) REVERT: J 45 LYS cc_start: 0.8573 (mmtp) cc_final: 0.8237 (mttp) REVERT: J 96 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7778 (mtpp) outliers start: 34 outliers final: 24 residues processed: 122 average time/residue: 0.5990 time to fit residues: 75.4520 Evaluate side-chains 122 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 47 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN H 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.105674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.089493 restraints weight = 6556.525| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.06 r_work: 0.3367 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4680 Z= 0.242 Angle : 0.658 6.748 6315 Z= 0.365 Chirality : 0.054 0.138 835 Planarity : 0.003 0.020 775 Dihedral : 6.057 25.815 679 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 7.02 % Allowed : 21.70 % Favored : 71.28 % 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 aren not related in a simple way. whole: -2.52 (0.29), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR H 39 PHE 0.019 0.004 PHE G 94 HIS 0.003 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 4680) covalent geometry : angle 0.65828 ( 6315) hydrogen bonds : bond 0.02827 ( 180) hydrogen bonds : angle 5.01135 ( 540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.114 Fit side-chains REVERT: A 58 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8196 (mttp) REVERT: A 62 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: B 58 LYS cc_start: 0.9069 (mttm) cc_final: 0.8808 (mttm) REVERT: C 58 LYS cc_start: 0.8621 (mtpt) cc_final: 0.8315 (mttm) REVERT: D 83 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7346 (tp30) REVERT: F 35 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7046 (tm-30) REVERT: G 44 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8532 (m) REVERT: G 57 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: H 46 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: H 83 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7355 (tp30) REVERT: I 58 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8253 (mttp) REVERT: J 35 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7168 (tp30) REVERT: J 45 LYS cc_start: 0.8589 (mmtp) cc_final: 0.8270 (mttp) REVERT: J 96 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7736 (mtpp) outliers start: 33 outliers final: 23 residues processed: 118 average time/residue: 0.5145 time to fit residues: 62.7489 Evaluate side-chains 119 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.104405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.089212 restraints weight = 6241.008| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.92 r_work: 0.3305 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 4680 Z= 0.373 Angle : 0.761 7.879 6315 Z= 0.421 Chirality : 0.057 0.175 835 Planarity : 0.003 0.023 775 Dihedral : 6.442 27.842 679 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 6.60 % Allowed : 21.91 % Favored : 71.49 % 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: -2.57 (0.29), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR F 39 PHE 0.022 0.005 PHE G 94 HIS 0.005 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00798 ( 4680) covalent geometry : angle 0.76052 ( 6315) hydrogen bonds : bond 0.03219 ( 180) hydrogen bonds : angle 5.09752 ( 540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8222 (mttp) REVERT: A 62 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: B 58 LYS cc_start: 0.9020 (mttm) cc_final: 0.8733 (mttm) REVERT: C 58 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8503 (mttm) REVERT: D 35 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7024 (tm-30) REVERT: D 83 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7375 (tp30) REVERT: F 35 GLU cc_start: 0.7423 (tm-30) cc_final: 0.6990 (tm-30) REVERT: G 57 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: H 83 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7327 (tp30) REVERT: I 58 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8172 (mttp) REVERT: J 35 GLU cc_start: 0.7445 (tm-30) cc_final: 0.6896 (tm-30) REVERT: J 45 LYS cc_start: 0.8585 (mmtp) cc_final: 0.8265 (mttp) REVERT: J 96 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7734 (mtpp) outliers start: 31 outliers final: 23 residues processed: 114 average time/residue: 0.5865 time to fit residues: 68.8500 Evaluate side-chains 117 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.106401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.090366 restraints weight = 6441.890| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.04 r_work: 0.3380 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4680 Z= 0.207 Angle : 0.685 8.395 6315 Z= 0.377 Chirality : 0.054 0.135 835 Planarity : 0.003 0.022 775 Dihedral : 6.132 26.262 679 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 5.74 % Allowed : 22.98 % Favored : 71.28 % 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 aren not related in a simple way. whole: -2.53 (0.29), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR H 39 PHE 0.017 0.004 PHE G 94 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 4680) covalent geometry : angle 0.68536 ( 6315) hydrogen bonds : bond 0.02726 ( 180) hydrogen bonds : angle 5.01065 ( 540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.129 Fit side-chains REVERT: A 58 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8152 (mttp) REVERT: B 58 LYS cc_start: 0.9022 (mttm) cc_final: 0.8748 (mttm) REVERT: C 58 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8335 (mttm) REVERT: D 58 LYS cc_start: 0.8951 (mttm) cc_final: 0.8671 (mttp) REVERT: D 83 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7288 (tp30) REVERT: F 35 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6896 (tm-30) REVERT: G 44 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8535 (m) REVERT: G 57 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: H 58 LYS cc_start: 0.8977 (mttm) cc_final: 0.8711 (mttp) REVERT: H 83 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7233 (tp30) REVERT: I 58 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8159 (mttp) REVERT: J 35 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7105 (tp30) REVERT: J 45 LYS cc_start: 0.8557 (mmtp) cc_final: 0.8231 (mttp) REVERT: J 96 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7684 (mtpp) outliers start: 27 outliers final: 21 residues processed: 115 average time/residue: 0.6042 time to fit residues: 71.7459 Evaluate side-chains 117 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 59 optimal weight: 0.0030 chunk 2 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.110739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.095992 restraints weight = 6231.287| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.93 r_work: 0.3446 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4680 Z= 0.164 Angle : 0.652 8.238 6315 Z= 0.359 Chirality : 0.053 0.134 835 Planarity : 0.003 0.020 775 Dihedral : 5.831 24.912 679 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.68 % Allowed : 24.04 % Favored : 71.28 % 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 aren not related in a simple way. whole: -2.47 (0.30), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR F 39 PHE 0.018 0.004 PHE D 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4680) covalent geometry : angle 0.65249 ( 6315) hydrogen bonds : bond 0.02462 ( 180) hydrogen bonds : angle 4.93865 ( 540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.53 seconds wall clock time: 30 minutes 56.41 seconds (1856.41 seconds total)