Starting phenix.real_space_refine on Wed Sep 17 16:04:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rgx_19162/09_2025/8rgx_19162_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rgx_19162/09_2025/8rgx_19162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rgx_19162/09_2025/8rgx_19162_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rgx_19162/09_2025/8rgx_19162_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rgx_19162/09_2025/8rgx_19162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rgx_19162/09_2025/8rgx_19162.map" } resolution = 3.2 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= 0.011 sd= 0.102 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 24 5.16 5 C 6216 2.51 5 N 1764 2.21 5 O 1920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9924 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "B" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "E" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "F" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "I" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "J" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "K" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "L" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 2.41, per 1000 atoms: 0.24 Number of scatterers: 9924 At special positions: 0 Unit cell: (117.3, 117.3, 62.22, 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 24 16.00 O 1920 8.00 N 1764 7.00 C 6216 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: 1.03 Conformation dependent library (CDL) restraints added in 434.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 86.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 43 through 64 removed outlier: 3.726A pdb=" N VAL A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 88 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 111 through 140 Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.509A pdb=" N VAL B 41 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 64 removed outlier: 3.741A pdb=" N VAL B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 88 Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 111 through 140 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 43 through 64 removed outlier: 3.717A pdb=" N VAL C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 64 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 88 Processing helix chain 'C' and resid 90 through 101 Processing helix chain 'C' and resid 111 through 140 Processing helix chain 'D' and resid 37 through 41 Processing helix chain 'D' and resid 43 through 64 removed outlier: 3.726A pdb=" N VAL D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 88 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 111 through 140 Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.513A pdb=" N VAL E 41 " --> pdb=" O THR E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 64 removed outlier: 3.740A pdb=" N VAL E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 88 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 111 through 140 Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 43 through 64 removed outlier: 3.719A pdb=" N VAL F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 88 Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 111 through 140 Processing helix chain 'G' and resid 37 through 41 Processing helix chain 'G' and resid 43 through 64 removed outlier: 3.724A pdb=" N VAL G 47 " --> pdb=" O GLN G 43 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA G 64 " --> pdb=" O GLU G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 88 Processing helix chain 'G' and resid 90 through 101 Processing helix chain 'G' and resid 111 through 140 Processing helix chain 'H' and resid 37 through 41 removed outlier: 3.512A pdb=" N VAL H 41 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 64 removed outlier: 3.741A pdb=" N VAL H 47 " --> pdb=" O GLN H 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 88 Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'H' and resid 111 through 140 Processing helix chain 'I' and resid 37 through 41 Processing helix chain 'I' and resid 43 through 64 removed outlier: 3.717A pdb=" N VAL I 47 " --> pdb=" O GLN I 43 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA I 64 " --> pdb=" O GLU I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 88 Processing helix chain 'I' and resid 90 through 101 Processing helix chain 'I' and resid 111 through 140 Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 43 through 64 removed outlier: 3.725A pdb=" N VAL J 47 " --> pdb=" O GLN J 43 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA J 64 " --> pdb=" O GLU J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 88 Processing helix chain 'J' and resid 90 through 101 Processing helix chain 'J' and resid 111 through 140 Processing helix chain 'K' and resid 37 through 41 removed outlier: 3.513A pdb=" N VAL K 41 " --> pdb=" O THR K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 64 removed outlier: 3.744A pdb=" N VAL K 47 " --> pdb=" O GLN K 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA K 64 " --> pdb=" O GLU K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 88 Processing helix chain 'K' and resid 90 through 101 Processing helix chain 'K' and resid 111 through 140 Processing helix chain 'L' and resid 37 through 41 Processing helix chain 'L' and resid 43 through 64 removed outlier: 3.716A pdb=" N VAL L 47 " --> pdb=" O GLN L 43 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA L 64 " --> pdb=" O GLU L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 88 Processing helix chain 'L' and resid 90 through 101 Processing helix chain 'L' and resid 111 through 140 836 hydrogen bonds defined for protein. 2448 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: 1.63 Time building geometry restraints manager: 1.33 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: 3528 1.34 - 1.46: 1011 1.46 - 1.57: 5469 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 10056 Sorted by residual: bond pdb=" CB LEU F 74 " pdb=" CG LEU F 74 " ideal model delta sigma weight residual 1.530 1.517 0.013 2.00e-02 2.50e+03 4.54e-01 bond pdb=" CB LEU C 74 " pdb=" CG LEU C 74 " ideal model delta sigma weight residual 1.530 1.517 0.013 2.00e-02 2.50e+03 4.39e-01 bond pdb=" CB LEU L 74 " pdb=" CG LEU L 74 " ideal model delta sigma weight residual 1.530 1.517 0.013 2.00e-02 2.50e+03 4.38e-01 bond pdb=" CB LEU B 74 " pdb=" CG LEU B 74 " ideal model delta sigma weight residual 1.530 1.517 0.013 2.00e-02 2.50e+03 4.26e-01 bond pdb=" CB LEU K 74 " pdb=" CG LEU K 74 " ideal model delta sigma weight residual 1.530 1.517 0.013 2.00e-02 2.50e+03 4.26e-01 ... (remaining 10051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.77: 12552 0.77 - 1.54: 850 1.54 - 2.31: 129 2.31 - 3.09: 62 3.09 - 3.86: 27 Bond angle restraints: 13620 Sorted by residual: angle pdb=" C MET E 48 " pdb=" N ARG E 49 " pdb=" CA ARG E 49 " ideal model delta sigma weight residual 120.29 118.36 1.93 1.42e+00 4.96e-01 1.85e+00 angle pdb=" N GLY B 88 " pdb=" CA GLY B 88 " pdb=" C GLY B 88 " ideal model delta sigma weight residual 113.18 116.40 -3.22 2.37e+00 1.78e-01 1.84e+00 angle pdb=" N GLY K 88 " pdb=" CA GLY K 88 " pdb=" C GLY K 88 " ideal model delta sigma weight residual 113.18 116.39 -3.21 2.37e+00 1.78e-01 1.84e+00 angle pdb=" C MET I 48 " pdb=" N ARG I 49 " pdb=" CA ARG I 49 " ideal model delta sigma weight residual 120.29 118.37 1.92 1.42e+00 4.96e-01 1.84e+00 angle pdb=" C MET L 48 " pdb=" N ARG L 49 " pdb=" CA ARG L 49 " ideal model delta sigma weight residual 120.29 118.37 1.92 1.42e+00 4.96e-01 1.84e+00 ... (remaining 13615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.81: 5553 12.81 - 25.63: 563 25.63 - 38.44: 100 38.44 - 51.26: 28 51.26 - 64.07: 20 Dihedral angle restraints: 6264 sinusoidal: 2616 harmonic: 3648 Sorted by residual: dihedral pdb=" CA ARG G 75 " pdb=" CB ARG G 75 " pdb=" CG ARG G 75 " pdb=" CD ARG G 75 " ideal model delta sinusoidal sigma weight residual -180.00 -121.43 -58.57 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG J 75 " pdb=" CB ARG J 75 " pdb=" CG ARG J 75 " pdb=" CD ARG J 75 " ideal model delta sinusoidal sigma weight residual -180.00 -121.44 -58.56 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG A 75 " pdb=" CB ARG A 75 " pdb=" CG ARG A 75 " pdb=" CD ARG A 75 " ideal model delta sinusoidal sigma weight residual -180.00 -121.44 -58.56 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 977 0.025 - 0.049: 454 0.049 - 0.074: 100 0.074 - 0.099: 47 0.099 - 0.123: 18 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CA VAL C 109 " pdb=" N VAL C 109 " pdb=" C VAL C 109 " pdb=" CB VAL C 109 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA VAL D 109 " pdb=" N VAL D 109 " pdb=" C VAL D 109 " pdb=" CB VAL D 109 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA VAL G 109 " pdb=" N VAL G 109 " pdb=" C VAL G 109 " pdb=" CB VAL G 109 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 1593 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 43 " 0.014 5.00e-02 4.00e+02 2.19e-02 7.65e-01 pdb=" N PRO H 44 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO H 44 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO H 44 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 43 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.53e-01 pdb=" N PRO B 44 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN K 43 " 0.014 5.00e-02 4.00e+02 2.16e-02 7.45e-01 pdb=" N PRO K 44 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO K 44 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO K 44 " 0.012 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2818 2.83 - 3.35: 10090 3.35 - 3.87: 16023 3.87 - 4.38: 18281 4.38 - 4.90: 32429 Nonbonded interactions: 79641 Sorted by model distance: nonbonded pdb=" NH1 ARG F 116 " pdb=" OE2 GLU G 60 " model vdw 2.316 3.120 nonbonded pdb=" NH1 ARG C 116 " pdb=" OE2 GLU D 60 " model vdw 2.317 3.120 nonbonded pdb=" OE2 GLU A 60 " pdb=" NH1 ARG L 116 " model vdw 2.318 3.120 nonbonded pdb=" NH1 ARG I 116 " pdb=" OE2 GLU J 60 " model vdw 2.319 3.120 nonbonded pdb=" OD1 ASP K 67 " pdb=" OG SER K 70 " model vdw 2.323 3.040 ... (remaining 79636 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: 0.04 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.820 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 0.004 0.019 10056 Z= 0.160 Angle : 0.480 3.858 13620 Z= 0.258 Chirality : 0.033 0.123 1596 Planarity : 0.004 0.022 1812 Dihedral : 11.005 64.071 3864 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.76 % Allowed : 4.73 % Favored : 94.51 % 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: 2.97 (0.23), residues: 1236 helix: 2.20 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : 0.23 (0.45), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 75 PHE 0.004 0.001 PHE E 138 TRP 0.002 0.001 TRP J 125 HIS 0.002 0.001 HIS K 131 Details of bonding type rmsd covalent geometry : bond 0.00357 (10056) covalent geometry : angle 0.47991 (13620) hydrogen bonds : bond 0.13469 ( 836) hydrogen bonds : angle 3.54709 ( 2448) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 397 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7172 (mmm160) REVERT: B 55 LYS cc_start: 0.8235 (tttp) cc_final: 0.7975 (tttp) REVERT: B 73 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7629 (tpt170) REVERT: B 121 GLN cc_start: 0.8482 (tt0) cc_final: 0.8239 (tt0) REVERT: C 46 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7929 (ttmt) REVERT: C 73 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7048 (mmm160) REVERT: C 84 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7411 (mm-30) REVERT: D 73 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7166 (mmm160) REVERT: E 55 LYS cc_start: 0.8235 (tttp) cc_final: 0.8016 (tttp) REVERT: E 73 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7629 (tpt170) REVERT: E 121 GLN cc_start: 0.8484 (tt0) cc_final: 0.8234 (tt0) REVERT: F 46 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7932 (ttmt) REVERT: F 73 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7045 (mmm160) REVERT: F 84 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7421 (mm-30) REVERT: G 73 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7163 (mmm160) REVERT: H 55 LYS cc_start: 0.8234 (tttp) cc_final: 0.7972 (tttp) REVERT: H 73 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7633 (tpt170) REVERT: H 121 GLN cc_start: 0.8485 (tt0) cc_final: 0.8239 (tt0) REVERT: I 46 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7930 (ttmt) REVERT: I 73 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7047 (mmm160) REVERT: I 84 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7421 (mm-30) REVERT: J 73 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7177 (mmm160) REVERT: K 55 LYS cc_start: 0.8233 (tttp) cc_final: 0.8016 (tttp) REVERT: K 121 GLN cc_start: 0.8485 (tt0) cc_final: 0.8243 (tt0) REVERT: L 46 LYS cc_start: 0.8312 (ttmt) cc_final: 0.7931 (ttmt) REVERT: L 73 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7041 (mmm160) REVERT: L 84 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7429 (mm-30) outliers start: 8 outliers final: 8 residues processed: 397 average time/residue: 0.1272 time to fit residues: 66.0761 Evaluate side-chains 323 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 315 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain L residue 82 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN B 119 GLN C 119 GLN D 119 GLN E 119 GLN F 119 GLN G 119 GLN H 119 GLN I 119 GLN J 119 GLN K 119 GLN L 119 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.155785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124591 restraints weight = 13960.823| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.08 r_work: 0.3243 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10056 Z= 0.145 Angle : 0.511 4.062 13620 Z= 0.270 Chirality : 0.031 0.109 1596 Planarity : 0.004 0.025 1812 Dihedral : 3.945 27.826 1372 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.22 % Allowed : 9.85 % Favored : 86.93 % 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: 3.81 (0.22), residues: 1236 helix: 2.76 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : 0.42 (0.45), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 75 PHE 0.003 0.001 PHE K 138 TRP 0.003 0.001 TRP A 125 HIS 0.001 0.001 HIS G 78 Details of bonding type rmsd covalent geometry : bond 0.00317 (10056) covalent geometry : angle 0.51055 (13620) hydrogen bonds : bond 0.04690 ( 836) hydrogen bonds : angle 3.12933 ( 2448) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 349 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7354 (tp30) cc_final: 0.7144 (tp30) REVERT: A 73 ARG cc_start: 0.8355 (mtp85) cc_final: 0.7233 (mmm160) REVERT: A 116 ARG cc_start: 0.8507 (mtm110) cc_final: 0.8183 (mtm110) REVERT: B 42 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7646 (mt-10) REVERT: B 55 LYS cc_start: 0.8580 (tttp) cc_final: 0.8365 (tttm) REVERT: B 73 ARG cc_start: 0.8421 (mtp85) cc_final: 0.7651 (tpt170) REVERT: B 116 ARG cc_start: 0.8549 (mtm110) cc_final: 0.8174 (mtm110) REVERT: C 72 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.8084 (m-40) REVERT: C 73 ARG cc_start: 0.8280 (mtp85) cc_final: 0.7235 (mmm160) REVERT: D 73 ARG cc_start: 0.8343 (mtp85) cc_final: 0.7224 (mmm160) REVERT: D 116 ARG cc_start: 0.8501 (mtm110) cc_final: 0.8176 (mtm110) REVERT: E 55 LYS cc_start: 0.8571 (tttp) cc_final: 0.8295 (tttm) REVERT: E 73 ARG cc_start: 0.8415 (mtp85) cc_final: 0.7613 (tpt170) REVERT: F 72 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.8083 (m-40) REVERT: F 73 ARG cc_start: 0.8277 (mtp85) cc_final: 0.7230 (mmm160) REVERT: F 94 ARG cc_start: 0.8035 (mtt90) cc_final: 0.7819 (ttm170) REVERT: G 73 ARG cc_start: 0.8322 (mtp85) cc_final: 0.7210 (mmm160) REVERT: G 116 ARG cc_start: 0.8495 (mtm110) cc_final: 0.8173 (mtm110) REVERT: H 55 LYS cc_start: 0.8567 (tttp) cc_final: 0.8349 (tttm) REVERT: H 73 ARG cc_start: 0.8411 (mtp85) cc_final: 0.7643 (tpt170) REVERT: I 72 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.8077 (m-40) REVERT: I 73 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7220 (mmm160) REVERT: I 94 ARG cc_start: 0.8047 (mtt90) cc_final: 0.7837 (ttm170) REVERT: J 73 ARG cc_start: 0.8342 (mtp85) cc_final: 0.7231 (mmm160) REVERT: J 116 ARG cc_start: 0.8498 (mtm110) cc_final: 0.8173 (mtm110) REVERT: K 55 LYS cc_start: 0.8606 (tttp) cc_final: 0.8325 (tttm) REVERT: K 73 ARG cc_start: 0.8420 (mtp85) cc_final: 0.7642 (tpt170) REVERT: K 116 ARG cc_start: 0.8549 (mtm110) cc_final: 0.8177 (mtm110) REVERT: L 72 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.8085 (m-40) REVERT: L 73 ARG cc_start: 0.8290 (mtp85) cc_final: 0.7240 (mmm160) REVERT: L 94 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7837 (ttm170) outliers start: 34 outliers final: 14 residues processed: 360 average time/residue: 0.1296 time to fit residues: 60.7016 Evaluate side-chains 318 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 300 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 72 ASN Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 90 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN D 119 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN G 119 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 GLN J 119 GLN ** K 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.158083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124261 restraints weight = 13619.704| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.52 r_work: 0.3240 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 10056 Z= 0.128 Angle : 0.479 4.191 13620 Z= 0.254 Chirality : 0.031 0.123 1596 Planarity : 0.004 0.022 1812 Dihedral : 3.226 12.594 1356 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.17 % Allowed : 10.61 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.63 (0.22), residues: 1236 helix: 3.58 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.41 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 75 PHE 0.003 0.001 PHE B 130 TRP 0.003 0.001 TRP A 125 HIS 0.002 0.001 HIS E 78 Details of bonding type rmsd covalent geometry : bond 0.00274 (10056) covalent geometry : angle 0.47873 (13620) hydrogen bonds : bond 0.04309 ( 836) hydrogen bonds : angle 2.94735 ( 2448) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 311 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8404 (mtp85) cc_final: 0.7177 (mmm160) REVERT: A 76 ASP cc_start: 0.8396 (m-30) cc_final: 0.8053 (m-30) REVERT: A 116 ARG cc_start: 0.8587 (mtm110) cc_final: 0.8240 (mtp-110) REVERT: B 42 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7734 (mt-10) REVERT: B 55 LYS cc_start: 0.8495 (tttp) cc_final: 0.8285 (tttm) REVERT: B 73 ARG cc_start: 0.8418 (mtp85) cc_final: 0.7618 (tpt170) REVERT: C 42 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7477 (mt-10) REVERT: C 73 ARG cc_start: 0.8312 (mtp85) cc_final: 0.7131 (mmm160) REVERT: D 73 ARG cc_start: 0.8403 (mtp85) cc_final: 0.7170 (mmm160) REVERT: D 76 ASP cc_start: 0.8395 (m-30) cc_final: 0.8049 (m-30) REVERT: D 116 ARG cc_start: 0.8589 (mtm110) cc_final: 0.8245 (mtp-110) REVERT: E 55 LYS cc_start: 0.8477 (tttp) cc_final: 0.8273 (tttm) REVERT: E 73 ARG cc_start: 0.8404 (mtp85) cc_final: 0.7608 (tpt170) REVERT: F 42 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7436 (mt-10) REVERT: F 72 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.8081 (m-40) REVERT: F 73 ARG cc_start: 0.8328 (mtp85) cc_final: 0.7147 (mmm160) REVERT: F 94 ARG cc_start: 0.7928 (mtt90) cc_final: 0.7662 (ttm170) REVERT: G 73 ARG cc_start: 0.8390 (mtp85) cc_final: 0.7169 (mmm160) REVERT: G 76 ASP cc_start: 0.8411 (m-30) cc_final: 0.8067 (m-30) REVERT: G 116 ARG cc_start: 0.8589 (mtm110) cc_final: 0.8236 (mtp-110) REVERT: H 55 LYS cc_start: 0.8499 (tttp) cc_final: 0.8293 (tttm) REVERT: H 73 ARG cc_start: 0.8399 (mtp85) cc_final: 0.7627 (tpt170) REVERT: I 42 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7429 (mt-10) REVERT: I 72 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.8069 (m-40) REVERT: I 73 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7148 (mmm160) REVERT: I 94 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7659 (ttm170) REVERT: J 73 ARG cc_start: 0.8395 (mtp85) cc_final: 0.7200 (mmm160) REVERT: J 76 ASP cc_start: 0.8352 (m-30) cc_final: 0.8005 (m-30) REVERT: J 116 ARG cc_start: 0.8579 (mtm110) cc_final: 0.8233 (mtp-110) REVERT: K 55 LYS cc_start: 0.8483 (tttp) cc_final: 0.8274 (tttm) REVERT: K 73 ARG cc_start: 0.8405 (mtp85) cc_final: 0.7614 (tpt170) REVERT: L 42 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7391 (mt-10) REVERT: L 72 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.8068 (m-40) REVERT: L 73 ARG cc_start: 0.8306 (mtp85) cc_final: 0.7144 (mmm160) REVERT: L 94 ARG cc_start: 0.7944 (mtt90) cc_final: 0.7692 (ttm170) outliers start: 44 outliers final: 26 residues processed: 336 average time/residue: 0.1315 time to fit residues: 57.7480 Evaluate side-chains 316 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 287 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 72 ASN Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 59 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 67 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 GLN ** K 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.158815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.125322 restraints weight = 13745.702| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.21 r_work: 0.3256 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10056 Z= 0.116 Angle : 0.466 4.011 13620 Z= 0.248 Chirality : 0.030 0.125 1596 Planarity : 0.003 0.018 1812 Dihedral : 3.198 13.062 1356 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.03 % Allowed : 12.03 % Favored : 84.94 % 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: 5.04 (0.22), residues: 1236 helix: 3.85 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.64 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 75 PHE 0.003 0.001 PHE L 138 TRP 0.003 0.001 TRP K 125 HIS 0.001 0.000 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00243 (10056) covalent geometry : angle 0.46634 (13620) hydrogen bonds : bond 0.03955 ( 836) hydrogen bonds : angle 2.81552 ( 2448) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 316 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 72 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7714 (m110) REVERT: A 73 ARG cc_start: 0.8415 (mtp85) cc_final: 0.7142 (mmm160) REVERT: A 76 ASP cc_start: 0.8320 (m-30) cc_final: 0.7960 (m-30) REVERT: A 116 ARG cc_start: 0.8550 (mtm110) cc_final: 0.8095 (mtp-110) REVERT: B 42 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7709 (mt-10) REVERT: B 73 ARG cc_start: 0.8385 (mtp85) cc_final: 0.7280 (mmm160) REVERT: C 46 LYS cc_start: 0.8385 (ttmt) cc_final: 0.8146 (ttmm) REVERT: C 73 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7129 (mmm160) REVERT: D 42 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7574 (mt-10) REVERT: D 72 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7737 (m110) REVERT: D 73 ARG cc_start: 0.8411 (mtp85) cc_final: 0.7150 (mmm160) REVERT: D 76 ASP cc_start: 0.8305 (m-30) cc_final: 0.7948 (m-30) REVERT: D 116 ARG cc_start: 0.8553 (mtm110) cc_final: 0.8112 (mtp-110) REVERT: E 55 LYS cc_start: 0.8451 (tttp) cc_final: 0.8249 (tttm) REVERT: E 73 ARG cc_start: 0.8377 (mtp85) cc_final: 0.7290 (mmm160) REVERT: F 73 ARG cc_start: 0.8323 (mtp85) cc_final: 0.7139 (mmm160) REVERT: F 94 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7637 (ttm170) REVERT: G 42 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7581 (mt-10) REVERT: G 72 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7729 (m110) REVERT: G 73 ARG cc_start: 0.8401 (mtp85) cc_final: 0.7131 (mmm160) REVERT: G 76 ASP cc_start: 0.8324 (m-30) cc_final: 0.7976 (m-30) REVERT: H 55 LYS cc_start: 0.8474 (tttp) cc_final: 0.8274 (tttm) REVERT: H 73 ARG cc_start: 0.8364 (mtp85) cc_final: 0.7617 (tpt170) REVERT: I 73 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7138 (mmm160) REVERT: I 94 ARG cc_start: 0.7917 (mtt90) cc_final: 0.7669 (ttm170) REVERT: J 42 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7559 (mt-10) REVERT: J 68 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6973 (tm-30) REVERT: J 72 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7678 (m110) REVERT: J 73 ARG cc_start: 0.8387 (mtp85) cc_final: 0.7133 (mmm160) REVERT: J 76 ASP cc_start: 0.8288 (m-30) cc_final: 0.7915 (m-30) REVERT: J 116 ARG cc_start: 0.8555 (mtm110) cc_final: 0.8111 (mtp-110) REVERT: K 55 LYS cc_start: 0.8471 (tttp) cc_final: 0.8264 (tttm) REVERT: K 73 ARG cc_start: 0.8372 (mtp85) cc_final: 0.7300 (mmm160) REVERT: L 42 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7431 (mt-10) REVERT: L 46 LYS cc_start: 0.8377 (ttmt) cc_final: 0.8145 (ttmm) REVERT: L 73 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7140 (mmm160) REVERT: L 94 ARG cc_start: 0.7964 (mtt90) cc_final: 0.7717 (ttm170) outliers start: 32 outliers final: 22 residues processed: 337 average time/residue: 0.1298 time to fit residues: 57.3969 Evaluate side-chains 321 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 295 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 11 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN B 119 GLN C 119 GLN D 119 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN G 119 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 GLN J 119 GLN ** K 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.156746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125809 restraints weight = 14006.301| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.06 r_work: 0.3262 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10056 Z= 0.126 Angle : 0.489 4.400 13620 Z= 0.259 Chirality : 0.031 0.113 1596 Planarity : 0.004 0.023 1812 Dihedral : 3.190 13.153 1356 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.55 % Allowed : 13.54 % Favored : 81.91 % 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 aren not related in a simple way. whole: 4.97 (0.22), residues: 1236 helix: 3.79 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.65 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 75 PHE 0.003 0.001 PHE G 130 TRP 0.003 0.001 TRP G 125 HIS 0.001 0.000 HIS J 78 Details of bonding type rmsd covalent geometry : bond 0.00275 (10056) covalent geometry : angle 0.48899 (13620) hydrogen bonds : bond 0.04064 ( 836) hydrogen bonds : angle 2.81092 ( 2448) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 314 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7010 (tm-30) REVERT: A 72 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7628 (m110) REVERT: A 73 ARG cc_start: 0.8268 (mtp85) cc_final: 0.7142 (mmm160) REVERT: A 76 ASP cc_start: 0.8206 (m-30) cc_final: 0.7865 (m-30) REVERT: A 116 ARG cc_start: 0.8402 (mtm110) cc_final: 0.8168 (mtm110) REVERT: B 73 ARG cc_start: 0.8389 (mtp85) cc_final: 0.7672 (tpt170) REVERT: B 84 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7370 (mm-30) REVERT: B 92 GLU cc_start: 0.6023 (tm-30) cc_final: 0.5763 (tm-30) REVERT: C 73 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7243 (mmm160) REVERT: D 68 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7016 (tm-30) REVERT: D 72 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7648 (m110) REVERT: D 73 ARG cc_start: 0.8280 (mtp85) cc_final: 0.7158 (mmm160) REVERT: D 76 ASP cc_start: 0.8205 (m-30) cc_final: 0.7865 (m-30) REVERT: D 116 ARG cc_start: 0.8419 (mtm110) cc_final: 0.8191 (mtm110) REVERT: E 55 LYS cc_start: 0.8610 (tttp) cc_final: 0.8390 (tttm) REVERT: F 72 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8080 (m-40) REVERT: F 73 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7200 (mmm160) REVERT: F 94 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7775 (ttm170) REVERT: G 68 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7049 (tm-30) REVERT: G 72 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7640 (m110) REVERT: G 73 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7123 (mmm160) REVERT: G 76 ASP cc_start: 0.8200 (m-30) cc_final: 0.7863 (m-30) REVERT: G 116 ARG cc_start: 0.8665 (mtm110) cc_final: 0.8161 (mtm110) REVERT: H 55 LYS cc_start: 0.8637 (tttp) cc_final: 0.8417 (tttm) REVERT: H 73 ARG cc_start: 0.8404 (mtp85) cc_final: 0.7670 (tpt170) REVERT: H 84 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7402 (mm-30) REVERT: H 92 GLU cc_start: 0.5996 (tm-30) cc_final: 0.5721 (tm-30) REVERT: I 72 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.8056 (m-40) REVERT: I 73 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7239 (mmm160) REVERT: I 94 ARG cc_start: 0.8041 (mtt90) cc_final: 0.7804 (ttm170) REVERT: J 68 GLU cc_start: 0.7387 (tm-30) cc_final: 0.7047 (tm-30) REVERT: J 72 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7642 (m110) REVERT: J 73 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7117 (mmm160) REVERT: J 76 ASP cc_start: 0.8232 (m-30) cc_final: 0.7881 (m-30) REVERT: J 116 ARG cc_start: 0.8412 (mtm110) cc_final: 0.8186 (mtm110) REVERT: K 55 LYS cc_start: 0.8608 (tttp) cc_final: 0.8394 (tttm) REVERT: K 73 ARG cc_start: 0.8390 (mtp85) cc_final: 0.7662 (tpt170) REVERT: K 84 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7405 (mm-30) REVERT: L 42 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7460 (mt-10) REVERT: L 72 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.8011 (m-40) REVERT: L 73 ARG cc_start: 0.8307 (mtp85) cc_final: 0.7238 (mmm160) outliers start: 48 outliers final: 34 residues processed: 346 average time/residue: 0.1260 time to fit residues: 57.0866 Evaluate side-chains 314 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 72 ASN Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN D 119 GLN E 119 GLN F 119 GLN G 119 GLN H 119 GLN I 119 GLN J 119 GLN K 119 GLN L 119 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.157418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127178 restraints weight = 14011.359| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.27 r_work: 0.3291 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10056 Z= 0.122 Angle : 0.501 7.499 13620 Z= 0.263 Chirality : 0.031 0.131 1596 Planarity : 0.004 0.027 1812 Dihedral : 3.162 12.692 1356 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.22 % Allowed : 16.10 % Favored : 80.68 % 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: 5.03 (0.22), residues: 1236 helix: 3.84 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.60 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 116 PHE 0.002 0.001 PHE H 138 TRP 0.003 0.001 TRP J 125 HIS 0.001 0.000 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00262 (10056) covalent geometry : angle 0.50122 (13620) hydrogen bonds : bond 0.03923 ( 836) hydrogen bonds : angle 2.75230 ( 2448) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 277 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7752 (m110) REVERT: A 73 ARG cc_start: 0.8253 (mtp85) cc_final: 0.7119 (mmm160) REVERT: A 76 ASP cc_start: 0.8151 (m-30) cc_final: 0.7829 (m-30) REVERT: A 116 ARG cc_start: 0.8367 (mtm110) cc_final: 0.8142 (mtm110) REVERT: B 73 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7646 (tpt170) REVERT: C 46 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8129 (tttp) REVERT: C 73 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7225 (mmm160) REVERT: D 72 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7747 (m110) REVERT: D 73 ARG cc_start: 0.8279 (mtp85) cc_final: 0.7146 (mmm160) REVERT: D 76 ASP cc_start: 0.8165 (m-30) cc_final: 0.7844 (m-30) REVERT: D 116 ARG cc_start: 0.8374 (mtm110) cc_final: 0.8155 (mtm110) REVERT: E 55 LYS cc_start: 0.8562 (tttp) cc_final: 0.8340 (tttm) REVERT: F 72 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.8062 (m-40) REVERT: F 73 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7173 (mmm160) REVERT: F 94 ARG cc_start: 0.7991 (mtt90) cc_final: 0.7780 (ttm170) REVERT: G 68 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7077 (tm-30) REVERT: G 72 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7651 (m110) REVERT: G 73 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7112 (mmm160) REVERT: G 76 ASP cc_start: 0.8178 (m-30) cc_final: 0.7861 (m-30) REVERT: G 116 ARG cc_start: 0.8673 (mtm110) cc_final: 0.8188 (mtp-110) REVERT: H 55 LYS cc_start: 0.8607 (tttp) cc_final: 0.8381 (tttm) REVERT: H 73 ARG cc_start: 0.8390 (mtp85) cc_final: 0.7656 (tpt170) REVERT: I 73 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7219 (mmm160) REVERT: I 94 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7791 (ttm170) REVERT: J 72 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7655 (m110) REVERT: J 73 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7042 (mmm160) REVERT: J 76 ASP cc_start: 0.8222 (m-30) cc_final: 0.7877 (m-30) REVERT: J 116 ARG cc_start: 0.8422 (mtm110) cc_final: 0.8210 (mtm110) REVERT: K 55 LYS cc_start: 0.8574 (tttp) cc_final: 0.8349 (tttm) REVERT: K 73 ARG cc_start: 0.8360 (mtp85) cc_final: 0.7642 (tpt170) REVERT: L 73 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7203 (mmm160) outliers start: 34 outliers final: 23 residues processed: 301 average time/residue: 0.1329 time to fit residues: 51.9460 Evaluate side-chains 286 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 51 optimal weight: 0.8980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN D 119 GLN F 119 GLN G 119 GLN I 119 GLN J 119 GLN L 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.157102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125942 restraints weight = 13949.515| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.08 r_work: 0.3279 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10056 Z= 0.122 Angle : 0.499 5.308 13620 Z= 0.264 Chirality : 0.031 0.122 1596 Planarity : 0.004 0.022 1812 Dihedral : 3.152 12.644 1356 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.60 % Allowed : 16.95 % Favored : 79.45 % 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: 5.02 (0.22), residues: 1236 helix: 3.84 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.58 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 116 PHE 0.002 0.001 PHE G 130 TRP 0.003 0.001 TRP G 125 HIS 0.001 0.000 HIS E 78 Details of bonding type rmsd covalent geometry : bond 0.00263 (10056) covalent geometry : angle 0.49879 (13620) hydrogen bonds : bond 0.03858 ( 836) hydrogen bonds : angle 2.73778 ( 2448) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 275 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7734 (m110) REVERT: A 73 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7102 (mmm160) REVERT: A 76 ASP cc_start: 0.8162 (m-30) cc_final: 0.7829 (m-30) REVERT: A 116 ARG cc_start: 0.8374 (mtm110) cc_final: 0.8156 (mtm110) REVERT: B 73 ARG cc_start: 0.8364 (mtp85) cc_final: 0.7699 (tpt170) REVERT: C 46 LYS cc_start: 0.8369 (ttmt) cc_final: 0.8089 (ttmm) REVERT: C 73 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7201 (mmm160) REVERT: D 72 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7761 (m110) REVERT: D 73 ARG cc_start: 0.8289 (mtp85) cc_final: 0.7142 (mmm160) REVERT: D 76 ASP cc_start: 0.8158 (m-30) cc_final: 0.7829 (m-30) REVERT: D 116 ARG cc_start: 0.8434 (mtm110) cc_final: 0.8223 (mtm110) REVERT: E 55 LYS cc_start: 0.8570 (tttp) cc_final: 0.8343 (tttm) REVERT: E 84 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7526 (mm-30) REVERT: F 72 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.8071 (m-40) REVERT: F 73 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7182 (mmm160) REVERT: F 94 ARG cc_start: 0.8020 (mtt90) cc_final: 0.7793 (ttm170) REVERT: G 72 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7732 (m110) REVERT: G 73 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7110 (mmm160) REVERT: G 76 ASP cc_start: 0.8162 (m-30) cc_final: 0.7834 (m-30) REVERT: H 55 LYS cc_start: 0.8639 (tttp) cc_final: 0.8351 (tttm) REVERT: H 73 ARG cc_start: 0.8394 (mtp85) cc_final: 0.7713 (tpt170) REVERT: I 72 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.8042 (m-40) REVERT: I 73 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7194 (mmm160) REVERT: I 94 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7783 (ttm170) REVERT: J 72 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7669 (m110) REVERT: J 73 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7070 (mmm160) REVERT: J 76 ASP cc_start: 0.8250 (m-30) cc_final: 0.7898 (m-30) REVERT: J 116 ARG cc_start: 0.8436 (mtm110) cc_final: 0.8216 (mtm110) REVERT: K 55 LYS cc_start: 0.8582 (tttp) cc_final: 0.8346 (tttm) REVERT: K 73 ARG cc_start: 0.8398 (mtp85) cc_final: 0.7714 (tpt170) REVERT: K 84 GLU cc_start: 0.8014 (tp30) cc_final: 0.7800 (mm-30) REVERT: L 72 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.8052 (m-40) REVERT: L 73 ARG cc_start: 0.8286 (mtp85) cc_final: 0.7214 (mmm160) REVERT: L 94 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7915 (ttm170) outliers start: 38 outliers final: 28 residues processed: 301 average time/residue: 0.1259 time to fit residues: 49.5359 Evaluate side-chains 299 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 72 ASN Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN D 119 GLN F 119 GLN G 119 GLN I 119 GLN J 119 GLN L 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.156774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125758 restraints weight = 13907.498| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.06 r_work: 0.3277 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10056 Z= 0.129 Angle : 0.517 6.141 13620 Z= 0.274 Chirality : 0.032 0.145 1596 Planarity : 0.004 0.024 1812 Dihedral : 3.163 14.215 1356 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.31 % Allowed : 17.90 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.98 (0.21), residues: 1236 helix: 3.84 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.47 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 116 PHE 0.002 0.001 PHE J 130 TRP 0.003 0.001 TRP D 125 HIS 0.001 0.000 HIS E 78 Details of bonding type rmsd covalent geometry : bond 0.00281 (10056) covalent geometry : angle 0.51692 (13620) hydrogen bonds : bond 0.03854 ( 836) hydrogen bonds : angle 2.74623 ( 2448) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7758 (m110) REVERT: A 73 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7100 (mmm160) REVERT: A 76 ASP cc_start: 0.8129 (m-30) cc_final: 0.7817 (m-30) REVERT: A 116 ARG cc_start: 0.8369 (mtm110) cc_final: 0.8150 (mtm110) REVERT: B 73 ARG cc_start: 0.8365 (mtp85) cc_final: 0.7714 (tpt170) REVERT: C 73 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7200 (mmm160) REVERT: D 72 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7778 (m110) REVERT: D 73 ARG cc_start: 0.8259 (mtp85) cc_final: 0.7131 (mmm160) REVERT: D 76 ASP cc_start: 0.8132 (m-30) cc_final: 0.7828 (m-30) REVERT: D 116 ARG cc_start: 0.8371 (mtm110) cc_final: 0.8150 (mtm110) REVERT: E 55 LYS cc_start: 0.8556 (tttp) cc_final: 0.8341 (tttm) REVERT: E 73 ARG cc_start: 0.8375 (mtp85) cc_final: 0.7632 (tpt170) REVERT: E 84 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7545 (mm-30) REVERT: F 73 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7184 (mmm160) REVERT: F 94 ARG cc_start: 0.8017 (mtt90) cc_final: 0.7790 (ttm170) REVERT: G 72 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7768 (m110) REVERT: G 73 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7126 (mmm160) REVERT: G 76 ASP cc_start: 0.8142 (m-30) cc_final: 0.7834 (m-30) REVERT: H 55 LYS cc_start: 0.8621 (tttp) cc_final: 0.8388 (tttm) REVERT: H 73 ARG cc_start: 0.8397 (mtp85) cc_final: 0.7720 (tpt170) REVERT: I 73 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7209 (mmm160) REVERT: I 94 ARG cc_start: 0.8011 (mtt90) cc_final: 0.7771 (ttm170) REVERT: J 72 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7697 (m110) REVERT: J 73 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7063 (mmm160) REVERT: J 76 ASP cc_start: 0.8246 (m-30) cc_final: 0.7898 (m-30) REVERT: J 116 ARG cc_start: 0.8435 (mtm110) cc_final: 0.8220 (mtm110) REVERT: K 55 LYS cc_start: 0.8591 (tttp) cc_final: 0.8368 (tttm) REVERT: K 73 ARG cc_start: 0.8405 (mtp85) cc_final: 0.7720 (tpt170) REVERT: K 84 GLU cc_start: 0.7983 (tp30) cc_final: 0.7778 (mm-30) REVERT: K 94 ARG cc_start: 0.7942 (ttm110) cc_final: 0.7731 (mtt90) REVERT: L 72 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.8024 (m-40) REVERT: L 73 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7194 (mmm160) outliers start: 35 outliers final: 29 residues processed: 295 average time/residue: 0.1298 time to fit residues: 49.9396 Evaluate side-chains 302 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 268 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 0.0270 chunk 52 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN D 119 GLN F 119 GLN G 119 GLN I 119 GLN J 119 GLN L 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.157040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126151 restraints weight = 13934.222| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.08 r_work: 0.3282 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10056 Z= 0.130 Angle : 0.534 7.901 13620 Z= 0.283 Chirality : 0.032 0.143 1596 Planarity : 0.004 0.023 1812 Dihedral : 3.119 12.783 1356 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.75 % Allowed : 18.75 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.99 (0.21), residues: 1236 helix: 3.87 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.31 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 94 PHE 0.002 0.000 PHE J 138 TRP 0.003 0.001 TRP G 125 HIS 0.001 0.000 HIS H 78 Details of bonding type rmsd covalent geometry : bond 0.00283 (10056) covalent geometry : angle 0.53356 (13620) hydrogen bonds : bond 0.03783 ( 836) hydrogen bonds : angle 2.73360 ( 2448) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 279 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7764 (m110) REVERT: A 73 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7094 (mmm160) REVERT: A 76 ASP cc_start: 0.8113 (m-30) cc_final: 0.7793 (m-30) REVERT: B 73 ARG cc_start: 0.8371 (mtp85) cc_final: 0.7724 (tpt170) REVERT: C 46 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8141 (ttmm) REVERT: C 73 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7195 (mmm160) REVERT: C 94 ARG cc_start: 0.8038 (ttm110) cc_final: 0.7672 (ttm170) REVERT: D 72 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7743 (m110) REVERT: D 73 ARG cc_start: 0.8259 (mtp85) cc_final: 0.7126 (mmm160) REVERT: D 76 ASP cc_start: 0.8104 (m-30) cc_final: 0.7785 (m-30) REVERT: E 55 LYS cc_start: 0.8549 (tttp) cc_final: 0.8332 (tttm) REVERT: E 73 ARG cc_start: 0.8369 (mtp85) cc_final: 0.7641 (tpt170) REVERT: E 94 ARG cc_start: 0.7944 (ttm110) cc_final: 0.7615 (mtt90) REVERT: F 73 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7191 (mmm160) REVERT: F 94 ARG cc_start: 0.7997 (mtt90) cc_final: 0.7781 (ttm170) REVERT: G 72 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7781 (m110) REVERT: G 73 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7122 (mmm160) REVERT: G 76 ASP cc_start: 0.8136 (m-30) cc_final: 0.7825 (m-30) REVERT: H 55 LYS cc_start: 0.8630 (tttp) cc_final: 0.8402 (tttm) REVERT: H 68 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7311 (tm-30) REVERT: H 73 ARG cc_start: 0.8412 (mtp85) cc_final: 0.7707 (tpt170) REVERT: I 73 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7191 (mmm160) REVERT: I 94 ARG cc_start: 0.8003 (mtt90) cc_final: 0.7772 (ttm170) REVERT: J 72 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7670 (m110) REVERT: J 73 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7069 (mmm160) REVERT: J 76 ASP cc_start: 0.8239 (m-30) cc_final: 0.7884 (m-30) REVERT: K 55 LYS cc_start: 0.8575 (tttp) cc_final: 0.8352 (tttm) REVERT: K 73 ARG cc_start: 0.8400 (mtp85) cc_final: 0.7718 (tpt170) REVERT: K 84 GLU cc_start: 0.7955 (tp30) cc_final: 0.7733 (mm-30) REVERT: K 94 ARG cc_start: 0.7947 (ttm110) cc_final: 0.7622 (mtt90) REVERT: L 73 ARG cc_start: 0.8263 (mtp85) cc_final: 0.7209 (mmm160) outliers start: 29 outliers final: 25 residues processed: 301 average time/residue: 0.1303 time to fit residues: 51.1250 Evaluate side-chains 299 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 270 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 80 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN D 119 GLN F 119 GLN G 119 GLN I 119 GLN J 119 GLN L 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.156494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125663 restraints weight = 13806.856| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.06 r_work: 0.3269 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10056 Z= 0.134 Angle : 0.538 5.748 13620 Z= 0.287 Chirality : 0.032 0.128 1596 Planarity : 0.004 0.026 1812 Dihedral : 3.142 12.678 1356 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.03 % Allowed : 18.47 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.94 (0.21), residues: 1236 helix: 3.83 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.29 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 94 PHE 0.002 0.001 PHE J 130 TRP 0.003 0.001 TRP G 125 HIS 0.001 0.000 HIS K 78 Details of bonding type rmsd covalent geometry : bond 0.00295 (10056) covalent geometry : angle 0.53847 (13620) hydrogen bonds : bond 0.03812 ( 836) hydrogen bonds : angle 2.76374 ( 2448) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7767 (m110) REVERT: A 73 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7119 (mmm160) REVERT: A 76 ASP cc_start: 0.8106 (m-30) cc_final: 0.7794 (m-30) REVERT: A 94 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7589 (mtm110) REVERT: B 73 ARG cc_start: 0.8386 (mtp85) cc_final: 0.7749 (tpt170) REVERT: B 94 ARG cc_start: 0.7930 (ttm110) cc_final: 0.7690 (mtt90) REVERT: C 73 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7684 (tpt170) REVERT: C 94 ARG cc_start: 0.8024 (ttm110) cc_final: 0.7710 (ttm170) REVERT: D 72 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7756 (m110) REVERT: D 73 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7128 (mmm160) REVERT: D 76 ASP cc_start: 0.8117 (m-30) cc_final: 0.7801 (m-30) REVERT: E 55 LYS cc_start: 0.8574 (tttp) cc_final: 0.8353 (tttm) REVERT: E 73 ARG cc_start: 0.8366 (mtp85) cc_final: 0.7650 (tpt170) REVERT: E 94 ARG cc_start: 0.7928 (ttm110) cc_final: 0.7535 (mtt90) REVERT: F 73 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7222 (mmm160) REVERT: F 94 ARG cc_start: 0.8007 (mtt90) cc_final: 0.7789 (ttm170) REVERT: G 72 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7761 (m110) REVERT: G 73 ARG cc_start: 0.8306 (mtp85) cc_final: 0.7133 (mmm160) REVERT: G 76 ASP cc_start: 0.8135 (m-30) cc_final: 0.7820 (m-30) REVERT: G 94 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7568 (mtm110) REVERT: H 55 LYS cc_start: 0.8662 (tttp) cc_final: 0.8428 (tttm) REVERT: H 73 ARG cc_start: 0.8392 (mtp85) cc_final: 0.7729 (tpt170) REVERT: I 73 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7210 (mmm160) REVERT: I 94 ARG cc_start: 0.8007 (mtt90) cc_final: 0.7787 (ttm170) REVERT: J 72 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7725 (m110) REVERT: J 73 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7077 (mmm160) REVERT: J 76 ASP cc_start: 0.8257 (m-30) cc_final: 0.7909 (m-30) REVERT: J 94 ARG cc_start: 0.7886 (ttm110) cc_final: 0.7664 (mtm110) REVERT: K 55 LYS cc_start: 0.8597 (tttp) cc_final: 0.8375 (tttm) REVERT: K 73 ARG cc_start: 0.8395 (mtp85) cc_final: 0.7730 (tpt170) REVERT: K 84 GLU cc_start: 0.7971 (tp30) cc_final: 0.7752 (mm-30) REVERT: K 94 ARG cc_start: 0.7875 (ttm110) cc_final: 0.7519 (mtt90) REVERT: L 40 LEU cc_start: 0.8294 (mm) cc_final: 0.7948 (mt) REVERT: L 72 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.8047 (m-40) REVERT: L 73 ARG cc_start: 0.8283 (mtp85) cc_final: 0.7219 (mmm160) outliers start: 32 outliers final: 27 residues processed: 297 average time/residue: 0.1290 time to fit residues: 50.3412 Evaluate side-chains 302 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN D 119 GLN F 119 GLN G 119 GLN I 119 GLN J 119 GLN L 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125320 restraints weight = 14080.415| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.11 r_work: 0.3266 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10056 Z= 0.136 Angle : 0.547 5.586 13620 Z= 0.294 Chirality : 0.032 0.123 1596 Planarity : 0.004 0.030 1812 Dihedral : 3.141 12.626 1356 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.84 % Allowed : 19.13 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.89 (0.21), residues: 1236 helix: 3.80 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.28 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 94 PHE 0.002 0.001 PHE J 130 TRP 0.003 0.001 TRP D 125 HIS 0.001 0.000 HIS H 78 Details of bonding type rmsd covalent geometry : bond 0.00298 (10056) covalent geometry : angle 0.54745 (13620) hydrogen bonds : bond 0.03799 ( 836) hydrogen bonds : angle 2.81541 ( 2448) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2186.20 seconds wall clock time: 38 minutes 7.95 seconds (2287.95 seconds total)