Starting phenix.real_space_refine on Wed Jan 22 06:55:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z1t_14452/01_2025/7z1t_14452.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z1t_14452/01_2025/7z1t_14452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z1t_14452/01_2025/7z1t_14452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z1t_14452/01_2025/7z1t_14452.map" model { file = "/net/cci-nas-00/data/ceres_data/7z1t_14452/01_2025/7z1t_14452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z1t_14452/01_2025/7z1t_14452.cif" } resolution = 2.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 96 5.16 5 C 12396 2.51 5 N 2892 2.21 5 O 3108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 18492 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 6.66, per 1000 atoms: 0.36 Number of scatterers: 18492 At special positions: 0 Unit cell: (100.062, 98.754, 158.922, 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 96 16.00 O 3108 8.00 N 2892 7.00 C 12396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 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: 5.26 Conformation dependent library (CDL) restraints added in 2.3 seconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 75.7% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 105 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 152 through 177 Processing helix chain 'A' and resid 202 through 235 Processing helix chain 'B' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 105 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 152 through 177 Processing helix chain 'B' and resid 202 through 235 Processing helix chain 'C' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 105 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 152 through 177 Processing helix chain 'C' and resid 202 through 235 Processing helix chain 'D' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 105 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 152 through 177 Processing helix chain 'D' and resid 202 through 235 Processing helix chain 'E' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 45 removed outlier: 4.391A pdb=" N VAL E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU E 42 " --> pdb=" O GLY E 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 105 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 152 through 177 Processing helix chain 'E' and resid 202 through 235 Processing helix chain 'F' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU F 42 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER F 43 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 105 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 152 through 177 Processing helix chain 'F' and resid 202 through 235 Processing helix chain 'G' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU G 42 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER G 43 " --> pdb=" O THR G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 73 through 105 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 152 through 177 Processing helix chain 'G' and resid 202 through 235 Processing helix chain 'H' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL H 41 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU H 42 " --> pdb=" O GLY H 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER H 43 " --> pdb=" O THR H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 73 through 105 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 152 through 177 Processing helix chain 'H' and resid 202 through 235 Processing helix chain 'I' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU I 7 " --> pdb=" O ASP I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU I 42 " --> pdb=" O GLY I 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER I 43 " --> pdb=" O THR I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 73 through 105 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 152 through 177 Processing helix chain 'I' and resid 202 through 235 Processing helix chain 'J' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU J 7 " --> pdb=" O ASP J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL J 41 " --> pdb=" O LEU J 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER J 43 " --> pdb=" O THR J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 73 through 105 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 152 through 177 Processing helix chain 'J' and resid 202 through 235 Processing helix chain 'K' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU K 7 " --> pdb=" O ASP K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL K 41 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU K 42 " --> pdb=" O GLY K 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER K 43 " --> pdb=" O THR K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 73 through 105 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 152 through 177 Processing helix chain 'K' and resid 202 through 235 Processing helix chain 'L' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU L 7 " --> pdb=" O ASP L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU L 42 " --> pdb=" O GLY L 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER L 43 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 73 through 105 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 152 through 177 Processing helix chain 'L' and resid 202 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 1416 hydrogen bonds defined for protein. 4176 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: 6.32 Time building geometry restraints manager: 5.92 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: 5391 1.34 - 1.46: 4689 1.46 - 1.58: 8808 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 19008 Sorted by residual: bond pdb=" C ASP G 190 " pdb=" N PRO G 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.76e+00 bond pdb=" C ASP A 190 " pdb=" N PRO A 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.76e+00 bond pdb=" C ASP E 190 " pdb=" N PRO E 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.69e+00 bond pdb=" C ASP K 190 " pdb=" N PRO K 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.69e+00 bond pdb=" C ASP B 190 " pdb=" N PRO B 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.69e+00 ... (remaining 19003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 24699 1.16 - 2.32: 879 2.32 - 3.48: 132 3.48 - 4.64: 54 4.64 - 5.80: 36 Bond angle restraints: 25800 Sorted by residual: angle pdb=" C VAL C 87 " pdb=" CA VAL C 87 " pdb=" CB VAL C 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL I 87 " pdb=" CA VAL I 87 " pdb=" CB VAL I 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL F 87 " pdb=" CA VAL F 87 " pdb=" CB VAL F 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL L 87 " pdb=" CA VAL L 87 " pdb=" CB VAL L 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL B 87 " pdb=" CA VAL B 87 " pdb=" CB VAL B 87 " ideal model delta sigma weight residual 113.70 110.62 3.08 9.50e-01 1.11e+00 1.05e+01 ... (remaining 25795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 9784 17.21 - 34.42: 918 34.42 - 51.63: 227 51.63 - 68.83: 12 68.83 - 86.04: 24 Dihedral angle restraints: 10965 sinusoidal: 4293 harmonic: 6672 Sorted by residual: dihedral pdb=" CA TYR E 177 " pdb=" C TYR E 177 " pdb=" N GLY E 178 " pdb=" CA GLY E 178 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA TYR D 177 " pdb=" C TYR D 177 " pdb=" N GLY D 178 " pdb=" CA GLY D 178 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA TYR A 177 " pdb=" C TYR A 177 " pdb=" N GLY A 178 " pdb=" CA GLY A 178 " ideal model delta harmonic sigma weight residual 180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 10962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1976 0.027 - 0.054: 598 0.054 - 0.080: 275 0.080 - 0.107: 79 0.107 - 0.134: 24 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA ARG D 202 " pdb=" N ARG D 202 " pdb=" C ARG D 202 " pdb=" CB ARG D 202 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ARG H 202 " pdb=" N ARG H 202 " pdb=" C ARG H 202 " pdb=" CB ARG H 202 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ARG J 202 " pdb=" N ARG J 202 " pdb=" C ARG J 202 " pdb=" CB ARG J 202 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 2949 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU K 205 " 0.004 2.00e-02 2.50e+03 9.14e-03 8.36e-01 pdb=" CD GLU K 205 " -0.016 2.00e-02 2.50e+03 pdb=" OE1 GLU K 205 " 0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU K 205 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 205 " -0.004 2.00e-02 2.50e+03 9.12e-03 8.31e-01 pdb=" CD GLU H 205 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLU H 205 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU H 205 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 205 " -0.004 2.00e-02 2.50e+03 9.06e-03 8.20e-01 pdb=" CD GLU B 205 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLU B 205 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU B 205 " -0.006 2.00e-02 2.50e+03 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 57 2.61 - 3.18: 15675 3.18 - 3.75: 30774 3.75 - 4.33: 38935 4.33 - 4.90: 64325 Nonbonded interactions: 149766 Sorted by model distance: nonbonded pdb=" SG CYS J 65 " pdb=" SG CYS J 187 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS E 65 " pdb=" SG CYS E 187 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS F 65 " pdb=" SG CYS F 187 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS I 65 " pdb=" SG CYS I 187 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS C 65 " pdb=" SG CYS C 187 " model vdw 2.032 3.760 ... (remaining 149761 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 37.910 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 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:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19008 Z= 0.177 Angle : 0.552 5.799 25800 Z= 0.307 Chirality : 0.034 0.134 2952 Planarity : 0.003 0.019 3096 Dihedral : 15.039 86.044 6636 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.17), residues: 2220 helix: 3.20 (0.11), residues: 1680 sheet: -0.64 (0.35), residues: 204 loop : -2.06 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 78 HIS 0.002 0.000 HIS G 74 PHE 0.012 0.001 PHE K 32 TYR 0.010 0.002 TYR A 66 ARG 0.003 0.000 ARG K 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 2.319 Fit side-chains outliers start: 0 outliers final: 6 residues processed: 372 average time/residue: 1.4390 time to fit residues: 595.5911 Evaluate side-chains 329 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 323 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain L residue 12 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 1.9990 chunk 163 optimal weight: 0.0870 chunk 90 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.102245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.072672 restraints weight = 28938.241| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.71 r_work: 0.2847 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 19008 Z= 0.170 Angle : 0.515 6.196 25800 Z= 0.261 Chirality : 0.035 0.109 2952 Planarity : 0.003 0.017 3096 Dihedral : 3.864 40.385 2448 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.09 % Allowed : 16.08 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.17), residues: 2220 helix: 3.37 (0.11), residues: 1692 sheet: -0.41 (0.36), residues: 204 loop : -2.30 (0.26), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 4 HIS 0.001 0.000 HIS E 74 PHE 0.014 0.001 PHE F 32 TYR 0.019 0.001 TYR B 98 ARG 0.002 0.000 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 346 time to evaluate : 2.249 Fit side-chains REVERT: A 4 TRP cc_start: 0.7774 (OUTLIER) cc_final: 0.6011 (t-100) REVERT: A 202 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8966 (mtt-85) REVERT: B 202 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.9007 (mtt-85) REVERT: C 4 TRP cc_start: 0.7770 (OUTLIER) cc_final: 0.6694 (t-100) REVERT: D 4 TRP cc_start: 0.7760 (OUTLIER) cc_final: 0.5986 (t-100) REVERT: D 202 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8967 (mtt-85) REVERT: E 202 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.9003 (mtt-85) REVERT: F 4 TRP cc_start: 0.7750 (OUTLIER) cc_final: 0.6681 (t-100) REVERT: G 4 TRP cc_start: 0.7760 (OUTLIER) cc_final: 0.5986 (t-100) REVERT: G 202 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8965 (mtt-85) REVERT: H 202 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.9003 (mtt-85) REVERT: I 4 TRP cc_start: 0.7774 (OUTLIER) cc_final: 0.6699 (t-100) REVERT: J 4 TRP cc_start: 0.7759 (OUTLIER) cc_final: 0.5987 (t-100) REVERT: J 202 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8962 (mtt-85) REVERT: K 202 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.9010 (mtt-85) REVERT: L 4 TRP cc_start: 0.7752 (OUTLIER) cc_final: 0.6676 (t-100) outliers start: 63 outliers final: 26 residues processed: 393 average time/residue: 1.4956 time to fit residues: 651.0682 Evaluate side-chains 350 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 308 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TRP Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 4 TRP Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 4 TRP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 4 TRP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 202 ARG Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 4 TRP Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 4 TRP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 202 ARG Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 4 TRP Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 203 optimal weight: 0.3980 chunk 173 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.100482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.071023 restraints weight = 28831.577| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.70 r_work: 0.2821 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 19008 Z= 0.174 Angle : 0.471 5.882 25800 Z= 0.239 Chirality : 0.035 0.106 2952 Planarity : 0.003 0.016 3096 Dihedral : 3.272 17.441 2436 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.09 % Allowed : 17.75 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.17), residues: 2220 helix: 3.41 (0.11), residues: 1692 sheet: -0.22 (0.36), residues: 204 loop : -2.30 (0.27), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 4 HIS 0.001 0.000 HIS G 74 PHE 0.013 0.001 PHE I 32 TYR 0.015 0.001 TYR B 98 ARG 0.003 0.001 ARG L 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 305 time to evaluate : 2.207 Fit side-chains REVERT: B 202 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8711 (ptp-170) REVERT: E 202 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8721 (ptp-170) REVERT: H 202 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8725 (ptp-170) REVERT: K 202 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8712 (ptp-170) outliers start: 63 outliers final: 26 residues processed: 360 average time/residue: 1.5139 time to fit residues: 602.6842 Evaluate side-chains 327 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 202 ARG Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 27 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN E 49 GLN H 49 GLN K 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.098392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.068963 restraints weight = 29101.233| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.72 r_work: 0.2776 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19008 Z= 0.209 Angle : 0.488 6.804 25800 Z= 0.248 Chirality : 0.035 0.112 2952 Planarity : 0.003 0.019 3096 Dihedral : 3.349 18.332 2436 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.77 % Allowed : 15.78 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.17), residues: 2220 helix: 3.40 (0.11), residues: 1692 sheet: -0.21 (0.36), residues: 204 loop : -2.19 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 4 HIS 0.002 0.001 HIS B 74 PHE 0.014 0.002 PHE J 32 TYR 0.016 0.001 TYR E 98 ARG 0.004 0.001 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 316 time to evaluate : 2.214 Fit side-chains REVERT: B 202 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8786 (ptp-170) REVERT: E 202 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8750 (ptp-170) REVERT: H 202 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8786 (ptp-170) REVERT: K 202 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8787 (ptp-170) outliers start: 77 outliers final: 38 residues processed: 377 average time/residue: 1.4683 time to fit residues: 621.4958 Evaluate side-chains 349 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 307 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 202 ARG Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 35 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 73 optimal weight: 0.0770 chunk 105 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 49 GLN L 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.070197 restraints weight = 29099.483| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.71 r_work: 0.2808 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 19008 Z= 0.165 Angle : 0.461 6.761 25800 Z= 0.233 Chirality : 0.034 0.113 2952 Planarity : 0.003 0.018 3096 Dihedral : 3.288 18.041 2436 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.75 % Allowed : 17.25 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.17), residues: 2220 helix: 3.55 (0.11), residues: 1692 sheet: -0.17 (0.37), residues: 204 loop : -2.14 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 174 HIS 0.001 0.000 HIS K 74 PHE 0.022 0.001 PHE D 232 TYR 0.016 0.001 TYR E 98 ARG 0.004 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 312 time to evaluate : 2.056 Fit side-chains REVERT: B 152 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8868 (tp) REVERT: B 202 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.9036 (mtt-85) REVERT: E 152 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8868 (tp) REVERT: E 202 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.9045 (mtt-85) REVERT: H 152 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8871 (tp) REVERT: H 202 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.9049 (mtt-85) REVERT: K 152 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8876 (tp) REVERT: K 202 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.9045 (mtt-85) outliers start: 56 outliers final: 24 residues processed: 362 average time/residue: 1.4549 time to fit residues: 584.2878 Evaluate side-chains 343 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 311 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 202 ARG Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 135 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.067555 restraints weight = 29424.341| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.71 r_work: 0.2751 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 19008 Z= 0.281 Angle : 0.518 6.707 25800 Z= 0.265 Chirality : 0.037 0.131 2952 Planarity : 0.003 0.020 3096 Dihedral : 3.469 19.034 2436 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.53 % Allowed : 16.23 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.17), residues: 2220 helix: 3.42 (0.11), residues: 1692 sheet: -0.26 (0.36), residues: 204 loop : -1.92 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 174 HIS 0.002 0.001 HIS C 74 PHE 0.025 0.002 PHE E 232 TYR 0.018 0.002 TYR E 98 ARG 0.003 0.001 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 314 time to evaluate : 2.227 Fit side-chains REVERT: A 232 PHE cc_start: 0.7706 (t80) cc_final: 0.7225 (m-80) REVERT: B 152 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8913 (tp) REVERT: B 202 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8827 (ptp-170) REVERT: D 232 PHE cc_start: 0.7700 (t80) cc_final: 0.7227 (m-80) REVERT: E 152 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8910 (tp) REVERT: E 202 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.8837 (ptp-170) REVERT: F 13 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8600 (tptp) REVERT: F 232 PHE cc_start: 0.7608 (t80) cc_final: 0.7192 (m-80) REVERT: G 232 PHE cc_start: 0.7700 (t80) cc_final: 0.7227 (m-80) REVERT: H 152 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8915 (tp) REVERT: H 202 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.8844 (ptp-170) REVERT: J 232 PHE cc_start: 0.7700 (t80) cc_final: 0.7225 (m-80) REVERT: K 152 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8919 (tp) REVERT: K 202 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.8833 (ptp-170) outliers start: 72 outliers final: 46 residues processed: 371 average time/residue: 1.4759 time to fit residues: 607.9040 Evaluate side-chains 362 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 307 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 202 ARG Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 135 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 49 GLN L 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.099506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.069940 restraints weight = 28679.945| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.66 r_work: 0.2793 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19008 Z= 0.142 Angle : 0.447 5.785 25800 Z= 0.227 Chirality : 0.034 0.104 2952 Planarity : 0.003 0.020 3096 Dihedral : 3.274 17.709 2436 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.60 % Allowed : 17.89 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.17), residues: 2220 helix: 3.56 (0.11), residues: 1692 sheet: -0.20 (0.36), residues: 204 loop : -2.00 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 174 HIS 0.001 0.000 HIS B 74 PHE 0.025 0.001 PHE E 232 TYR 0.015 0.001 TYR B 98 ARG 0.004 0.000 ARG F 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 326 time to evaluate : 2.186 Fit side-chains REVERT: A 232 PHE cc_start: 0.7682 (t80) cc_final: 0.7174 (m-80) REVERT: B 98 TYR cc_start: 0.8560 (m-80) cc_final: 0.8334 (m-80) REVERT: B 152 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8841 (tp) REVERT: C 232 PHE cc_start: 0.7574 (t80) cc_final: 0.7140 (m-80) REVERT: D 232 PHE cc_start: 0.7684 (t80) cc_final: 0.7176 (m-80) REVERT: E 98 TYR cc_start: 0.8546 (m-80) cc_final: 0.8318 (m-80) REVERT: E 152 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8837 (tp) REVERT: F 13 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8587 (tptp) REVERT: F 232 PHE cc_start: 0.7562 (t80) cc_final: 0.7146 (m-80) REVERT: G 232 PHE cc_start: 0.7684 (t80) cc_final: 0.7176 (m-80) REVERT: H 98 TYR cc_start: 0.8564 (m-80) cc_final: 0.8341 (m-80) REVERT: H 152 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8841 (tp) REVERT: I 232 PHE cc_start: 0.7576 (t80) cc_final: 0.7137 (m-80) REVERT: J 232 PHE cc_start: 0.7681 (t80) cc_final: 0.7179 (m-80) REVERT: K 98 TYR cc_start: 0.8559 (m-80) cc_final: 0.8334 (m-80) REVERT: K 152 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8838 (tp) REVERT: L 232 PHE cc_start: 0.7587 (t80) cc_final: 0.7151 (m-80) outliers start: 53 outliers final: 34 residues processed: 369 average time/residue: 1.4891 time to fit residues: 611.7747 Evaluate side-chains 351 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 312 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 161 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN F 49 GLN I 49 GLN L 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.097411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.067620 restraints weight = 29124.406| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.67 r_work: 0.2743 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19008 Z= 0.223 Angle : 0.497 7.243 25800 Z= 0.250 Chirality : 0.035 0.114 2952 Planarity : 0.003 0.019 3096 Dihedral : 3.370 18.429 2436 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.45 % Allowed : 17.84 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.17), residues: 2220 helix: 3.49 (0.11), residues: 1692 sheet: -0.20 (0.36), residues: 204 loop : -1.95 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 174 HIS 0.001 0.000 HIS A 74 PHE 0.028 0.002 PHE K 232 TYR 0.016 0.001 TYR B 98 ARG 0.004 0.001 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 2.068 Fit side-chains REVERT: A 232 PHE cc_start: 0.7700 (t80) cc_final: 0.7190 (m-80) REVERT: B 98 TYR cc_start: 0.8559 (m-80) cc_final: 0.8322 (m-80) REVERT: B 152 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8877 (tp) REVERT: C 232 PHE cc_start: 0.7588 (t80) cc_final: 0.7129 (m-80) REVERT: D 232 PHE cc_start: 0.7700 (t80) cc_final: 0.7187 (m-80) REVERT: E 98 TYR cc_start: 0.8563 (m-80) cc_final: 0.8324 (m-80) REVERT: E 152 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8871 (tp) REVERT: F 13 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8563 (tptp) REVERT: F 232 PHE cc_start: 0.7568 (t80) cc_final: 0.7135 (m-80) REVERT: G 232 PHE cc_start: 0.7701 (t80) cc_final: 0.7187 (m-80) REVERT: H 98 TYR cc_start: 0.8572 (m-80) cc_final: 0.8335 (m-80) REVERT: H 152 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8881 (tp) REVERT: H 232 PHE cc_start: 0.7667 (t80) cc_final: 0.7081 (m-80) REVERT: I 232 PHE cc_start: 0.7592 (t80) cc_final: 0.7132 (m-80) REVERT: J 232 PHE cc_start: 0.7701 (t80) cc_final: 0.7187 (m-80) REVERT: K 98 TYR cc_start: 0.8570 (m-80) cc_final: 0.8332 (m-80) REVERT: K 152 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8857 (tp) REVERT: L 232 PHE cc_start: 0.7598 (t80) cc_final: 0.7138 (m-80) outliers start: 50 outliers final: 28 residues processed: 339 average time/residue: 1.4885 time to fit residues: 559.5620 Evaluate side-chains 335 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 302 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 207 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 179 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.067230 restraints weight = 29194.002| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.68 r_work: 0.2734 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19008 Z= 0.235 Angle : 0.498 7.495 25800 Z= 0.252 Chirality : 0.035 0.116 2952 Planarity : 0.003 0.018 3096 Dihedral : 3.399 18.625 2436 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.16 % Allowed : 17.99 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.17), residues: 2220 helix: 3.46 (0.11), residues: 1692 sheet: -0.20 (0.37), residues: 204 loop : -2.00 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 174 HIS 0.002 0.001 HIS K 74 PHE 0.030 0.002 PHE E 232 TYR 0.015 0.002 TYR B 98 ARG 0.004 0.001 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 313 time to evaluate : 2.335 Fit side-chains REVERT: A 232 PHE cc_start: 0.7650 (t80) cc_final: 0.7210 (m-80) REVERT: B 98 TYR cc_start: 0.8566 (m-80) cc_final: 0.8338 (m-80) REVERT: B 152 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8872 (tp) REVERT: B 232 PHE cc_start: 0.7695 (t80) cc_final: 0.7110 (m-80) REVERT: C 232 PHE cc_start: 0.7636 (t80) cc_final: 0.7159 (m-80) REVERT: D 232 PHE cc_start: 0.7656 (t80) cc_final: 0.7212 (m-80) REVERT: E 98 TYR cc_start: 0.8571 (m-80) cc_final: 0.8340 (m-80) REVERT: E 152 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8869 (tp) REVERT: E 232 PHE cc_start: 0.7690 (t80) cc_final: 0.7101 (m-80) REVERT: F 13 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8556 (tptp) REVERT: F 232 PHE cc_start: 0.7615 (t80) cc_final: 0.7161 (m-80) REVERT: G 232 PHE cc_start: 0.7652 (t80) cc_final: 0.7210 (m-80) REVERT: H 98 TYR cc_start: 0.8590 (m-80) cc_final: 0.8359 (m-80) REVERT: H 152 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8872 (tp) REVERT: H 232 PHE cc_start: 0.7698 (t80) cc_final: 0.7112 (m-80) REVERT: I 232 PHE cc_start: 0.7639 (t80) cc_final: 0.7162 (m-80) REVERT: J 232 PHE cc_start: 0.7656 (t80) cc_final: 0.7215 (m-80) REVERT: K 98 TYR cc_start: 0.8580 (m-80) cc_final: 0.8346 (m-80) REVERT: K 152 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8870 (tp) REVERT: K 232 PHE cc_start: 0.7683 (t80) cc_final: 0.7102 (m-80) REVERT: L 232 PHE cc_start: 0.7628 (t80) cc_final: 0.7157 (m-80) outliers start: 44 outliers final: 35 residues processed: 356 average time/residue: 1.4528 time to fit residues: 577.4242 Evaluate side-chains 349 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 309 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 53 optimal weight: 8.9990 chunk 184 optimal weight: 0.7980 chunk 167 optimal weight: 0.1980 chunk 153 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.097901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.067823 restraints weight = 28876.576| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.69 r_work: 0.2753 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19008 Z= 0.198 Angle : 0.481 6.179 25800 Z= 0.244 Chirality : 0.034 0.110 2952 Planarity : 0.003 0.019 3096 Dihedral : 3.369 18.112 2436 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.21 % Allowed : 17.40 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.17), residues: 2220 helix: 3.49 (0.11), residues: 1692 sheet: -0.20 (0.36), residues: 204 loop : -2.00 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 174 HIS 0.001 0.000 HIS E 74 PHE 0.028 0.002 PHE E 232 TYR 0.014 0.001 TYR E 98 ARG 0.004 0.000 ARG H 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 319 time to evaluate : 2.465 Fit side-chains REVERT: A 232 PHE cc_start: 0.7631 (t80) cc_final: 0.7165 (m-80) REVERT: B 98 TYR cc_start: 0.8612 (m-80) cc_final: 0.8374 (m-80) REVERT: B 152 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8900 (tp) REVERT: B 232 PHE cc_start: 0.7672 (t80) cc_final: 0.7108 (m-80) REVERT: C 232 PHE cc_start: 0.7588 (t80) cc_final: 0.7106 (m-80) REVERT: D 232 PHE cc_start: 0.7636 (t80) cc_final: 0.7166 (m-80) REVERT: E 98 TYR cc_start: 0.8621 (m-80) cc_final: 0.8379 (m-80) REVERT: E 152 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8900 (tp) REVERT: E 232 PHE cc_start: 0.7652 (t80) cc_final: 0.7100 (m-80) REVERT: F 13 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8548 (tptp) REVERT: F 232 PHE cc_start: 0.7563 (t80) cc_final: 0.7107 (m-80) REVERT: G 12 ASP cc_start: 0.8827 (t0) cc_final: 0.8555 (p0) REVERT: G 232 PHE cc_start: 0.7633 (t80) cc_final: 0.7163 (m-80) REVERT: H 98 TYR cc_start: 0.8626 (m-80) cc_final: 0.8387 (m-80) REVERT: H 152 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8898 (tp) REVERT: H 232 PHE cc_start: 0.7654 (t80) cc_final: 0.7100 (m-80) REVERT: I 232 PHE cc_start: 0.7578 (t80) cc_final: 0.7088 (m-80) REVERT: J 232 PHE cc_start: 0.7636 (t80) cc_final: 0.7171 (m-80) REVERT: K 98 TYR cc_start: 0.8623 (m-80) cc_final: 0.8382 (m-80) REVERT: K 152 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8906 (tp) REVERT: K 232 PHE cc_start: 0.7646 (t80) cc_final: 0.7104 (m-80) REVERT: L 232 PHE cc_start: 0.7580 (t80) cc_final: 0.7114 (m-80) outliers start: 45 outliers final: 37 residues processed: 363 average time/residue: 1.4293 time to fit residues: 578.6731 Evaluate side-chains 360 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 318 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.6038 > 50: distance: 28 - 138: 34.038 distance: 31 - 135: 31.962 distance: 79 - 132: 36.720 distance: 82 - 129: 34.414 distance: 94 - 117: 37.015 distance: 97 - 114: 37.450 distance: 110 - 114: 34.578 distance: 114 - 115: 39.914 distance: 115 - 116: 38.746 distance: 115 - 118: 39.944 distance: 116 - 121: 56.157 distance: 118 - 120: 40.616 distance: 121 - 122: 39.360 distance: 122 - 123: 38.833 distance: 122 - 125: 38.619 distance: 123 - 124: 17.797 distance: 123 - 129: 39.737 distance: 125 - 126: 41.392 distance: 126 - 127: 19.163 distance: 126 - 128: 18.057 distance: 129 - 130: 38.889 distance: 130 - 131: 56.847 distance: 130 - 133: 48.320 distance: 131 - 135: 55.704 distance: 133 - 134: 10.731 distance: 135 - 136: 70.199 distance: 136 - 137: 56.052 distance: 136 - 139: 55.913 distance: 137 - 138: 38.982 distance: 139 - 140: 49.407 distance: 140 - 141: 40.737 distance: 140 - 142: 33.500 distance: 141 - 143: 44.517 distance: 144 - 145: 39.485 distance: 146 - 147: 56.465 distance: 147 - 148: 57.876 distance: 148 - 154: 69.617 distance: 151 - 152: 49.329 distance: 151 - 153: 55.971 distance: 154 - 155: 40.096 distance: 155 - 156: 56.921 distance: 155 - 158: 40.276 distance: 156 - 157: 56.293 distance: 160 - 161: 39.390 distance: 161 - 162: 57.679 distance: 161 - 164: 39.276 distance: 162 - 171: 38.986 distance: 163 - 194: 32.540 distance: 164 - 165: 41.522 distance: 165 - 166: 58.333 distance: 166 - 167: 41.427 distance: 168 - 169: 56.951 distance: 168 - 170: 40.278 distance: 171 - 172: 69.538 distance: 171 - 177: 40.294 distance: 172 - 173: 55.799 distance: 173 - 174: 23.846 distance: 173 - 178: 39.773 distance: 174 - 203: 28.073 distance: 176 - 177: 57.697 distance: 178 - 179: 21.954 distance: 179 - 180: 23.867 distance: 179 - 182: 42.887 distance: 181 - 210: 34.544 distance: 182 - 184: 45.715 distance: 186 - 189: 40.352 distance: 187 - 188: 40.146 distance: 187 - 194: 35.949 distance: 188 - 217: 32.008 distance: 189 - 190: 39.615 distance: 190 - 191: 17.992 distance: 191 - 192: 16.473 distance: 191 - 193: 17.655