Starting phenix.real_space_refine on Fri Sep 27 01:18:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/09_2024/5flu_3222.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/09_2024/5flu_3222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/09_2024/5flu_3222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/09_2024/5flu_3222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/09_2024/5flu_3222.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/09_2024/5flu_3222.cif" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 0.582 sd= 0.540 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 39 5.16 5 C 9399 2.51 5 N 2548 2.21 5 O 3146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15132 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1164 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L Time building chain proxies: 3.62, per 1000 atoms: 0.24 Number of scatterers: 15132 At special positions: 0 Unit cell: (95.7, 94.6, 145.2, 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 39 16.00 O 3146 8.00 N 2548 7.00 C 9399 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 61 " 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: 3.21 Conformation dependent library (CDL) restraints added in 1.8 seconds 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 39 sheets defined 11.8% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 63 through 70 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 63 through 70 Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 63 through 70 Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 63 through 70 Processing helix chain 'E' and resid 25 through 29 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 63 through 70 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 63 through 70 Processing helix chain 'G' and resid 25 through 29 Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 63 through 70 Processing helix chain 'H' and resid 25 through 29 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 63 through 70 Processing helix chain 'I' and resid 25 through 29 Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 63 through 70 Processing helix chain 'J' and resid 25 through 29 Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 63 through 70 Processing helix chain 'K' and resid 25 through 29 Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 63 through 70 Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 63 through 70 Processing helix chain 'M' and resid 25 through 29 Processing helix chain 'M' and resid 40 through 45 Processing helix chain 'M' and resid 63 through 70 Processing sheet with id=HA, first strand: chain 'H' and resid 30 through 39 removed outlier: 5.810A pdb=" N THR A 16 " --> pdb=" O PHE H 35 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN H 37 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A 18 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER H 39 " --> pdb=" O VAL A 18 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AB, first strand: chain 'A' and resid 30 through 39 removed outlier: 5.810A pdb=" N THR G 16 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN A 37 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL G 18 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER A 39 " --> pdb=" O VAL G 18 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=CA, first strand: chain 'C' and resid 30 through 39 removed outlier: 5.811A pdb=" N THR B 16 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN C 37 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 18 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER C 39 " --> pdb=" O VAL B 18 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=BB, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=BC, first strand: chain 'B' and resid 122 through 123 Processing sheet with id=DA, first strand: chain 'D' and resid 30 through 39 removed outlier: 5.809A pdb=" N THR C 16 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN D 37 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL C 18 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER D 39 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 23 through 24 Processing sheet with id=CC, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=EA, first strand: chain 'E' and resid 30 through 39 removed outlier: 5.810A pdb=" N THR D 16 " --> pdb=" O PHE E 35 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN E 37 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 18 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER E 39 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing sheet with id=DB, first strand: chain 'D' and resid 23 through 24 Processing sheet with id=DC, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=FA, first strand: chain 'F' and resid 30 through 39 removed outlier: 5.810A pdb=" N THR E 16 " --> pdb=" O PHE F 35 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN F 37 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 18 " --> pdb=" O GLN F 37 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER F 39 " --> pdb=" O VAL E 18 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 23 through 24 Processing sheet with id=EC, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=GA, first strand: chain 'G' and resid 30 through 39 removed outlier: 5.810A pdb=" N THR F 16 " --> pdb=" O PHE G 35 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN G 37 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL F 18 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER G 39 " --> pdb=" O VAL F 18 " (cutoff:3.500A) Processing sheet with id=FB, first strand: chain 'F' and resid 23 through 24 Processing sheet with id=FC, first strand: chain 'F' and resid 52 through 53 Processing sheet with id=GB, first strand: chain 'G' and resid 23 through 24 Processing sheet with id=GC, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=IA, first strand: chain 'I' and resid 30 through 39 removed outlier: 5.809A pdb=" N THR H 16 " --> pdb=" O PHE I 35 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN I 37 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL H 18 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N SER I 39 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=HB, first strand: chain 'H' and resid 23 through 24 Processing sheet with id=HC, first strand: chain 'H' and resid 52 through 53 Processing sheet with id=JA, first strand: chain 'J' and resid 30 through 39 removed outlier: 5.810A pdb=" N THR I 16 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN J 37 " --> pdb=" O THR I 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL I 18 " --> pdb=" O GLN J 37 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER J 39 " --> pdb=" O VAL I 18 " (cutoff:3.500A) Processing sheet with id=IB, first strand: chain 'I' and resid 23 through 24 Processing sheet with id=IC, first strand: chain 'I' and resid 52 through 53 Processing sheet with id=KA, first strand: chain 'K' and resid 30 through 39 removed outlier: 5.809A pdb=" N THR J 16 " --> pdb=" O PHE K 35 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN K 37 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL J 18 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER K 39 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing sheet with id=JB, first strand: chain 'J' and resid 23 through 24 Processing sheet with id=JC, first strand: chain 'J' and resid 52 through 53 Processing sheet with id=LA, first strand: chain 'L' and resid 30 through 39 removed outlier: 5.809A pdb=" N THR K 16 " --> pdb=" O PHE L 35 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN L 37 " --> pdb=" O THR K 16 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL K 18 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER L 39 " --> pdb=" O VAL K 18 " (cutoff:3.500A) Processing sheet with id=KB, first strand: chain 'K' and resid 23 through 24 Processing sheet with id=KC, first strand: chain 'K' and resid 52 through 53 Processing sheet with id=MA, first strand: chain 'M' and resid 30 through 39 removed outlier: 5.810A pdb=" N THR L 16 " --> pdb=" O PHE M 35 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN M 37 " --> pdb=" O THR L 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL L 18 " --> pdb=" O GLN M 37 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER M 39 " --> pdb=" O VAL L 18 " (cutoff:3.500A) Processing sheet with id=LB, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=LC, first strand: chain 'L' and resid 52 through 53 Processing sheet with id=MB, first strand: chain 'M' and resid 23 through 24 Processing sheet with id=MC, first strand: chain 'M' and resid 52 through 53 561 hydrogen bonds defined for protein. 1407 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: 4.17 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2962 1.32 - 1.44: 3421 1.44 - 1.57: 8905 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 15340 Sorted by residual: bond pdb=" CG ASP D 19 " pdb=" OD2 ASP D 19 " ideal model delta sigma weight residual 1.249 1.205 0.044 1.90e-02 2.77e+03 5.35e+00 bond pdb=" CD GLU A 118 " pdb=" OE1 GLU A 118 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.17e+00 bond pdb=" CG ASP M 19 " pdb=" OD2 ASP M 19 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.13e+00 bond pdb=" CG ASP E 19 " pdb=" OD2 ASP E 19 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.12e+00 bond pdb=" CG ASP B 19 " pdb=" OD2 ASP B 19 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.10e+00 ... (remaining 15335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 17682 1.27 - 2.53: 2619 2.53 - 3.80: 382 3.80 - 5.06: 78 5.06 - 6.33: 26 Bond angle restraints: 20787 Sorted by residual: angle pdb=" C ALA C 108 " pdb=" CA ALA C 108 " pdb=" CB ALA C 108 " ideal model delta sigma weight residual 116.54 110.21 6.33 1.15e+00 7.56e-01 3.03e+01 angle pdb=" C ALA K 108 " pdb=" CA ALA K 108 " pdb=" CB ALA K 108 " ideal model delta sigma weight residual 116.54 110.22 6.32 1.15e+00 7.56e-01 3.02e+01 angle pdb=" C ALA G 108 " pdb=" CA ALA G 108 " pdb=" CB ALA G 108 " ideal model delta sigma weight residual 116.54 110.23 6.31 1.15e+00 7.56e-01 3.01e+01 angle pdb=" C ALA J 108 " pdb=" CA ALA J 108 " pdb=" CB ALA J 108 " ideal model delta sigma weight residual 116.54 110.25 6.29 1.15e+00 7.56e-01 2.99e+01 angle pdb=" C ALA D 108 " pdb=" CA ALA D 108 " pdb=" CB ALA D 108 " ideal model delta sigma weight residual 116.54 110.25 6.29 1.15e+00 7.56e-01 2.99e+01 ... (remaining 20782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 8639 16.78 - 33.56: 267 33.56 - 50.34: 26 50.34 - 67.12: 28 67.12 - 83.89: 65 Dihedral angle restraints: 9025 sinusoidal: 3227 harmonic: 5798 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 61 " pdb=" CB CYS A 61 " ideal model delta sinusoidal sigma weight residual -86.00 -54.99 -31.01 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CA ALA C 1 " pdb=" C ALA C 1 " pdb=" N PRO C 2 " pdb=" CA PRO C 2 " ideal model delta harmonic sigma weight residual -180.00 -163.11 -16.89 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ALA D 1 " pdb=" C ALA D 1 " pdb=" N PRO D 2 " pdb=" CA PRO D 2 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 9022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1790 0.025 - 0.049: 110 0.049 - 0.074: 102 0.074 - 0.099: 205 0.099 - 0.123: 224 Chirality restraints: 2431 Sorted by residual: chirality pdb=" CA VAL M 112 " pdb=" N VAL M 112 " pdb=" C VAL M 112 " pdb=" CB VAL M 112 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA VAL G 112 " pdb=" N VAL G 112 " pdb=" C VAL G 112 " pdb=" CB VAL G 112 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 2428 not shown) Planarity restraints: 2782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA J 1 " -0.063 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO J 2 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO J 2 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO J 2 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 1 " 0.062 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO I 2 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO I 2 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO I 2 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 1 " -0.062 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A 2 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 2 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 2 " -0.050 5.00e-02 4.00e+02 ... (remaining 2779 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 189 2.61 - 3.18: 14210 3.18 - 3.75: 23128 3.75 - 4.33: 34607 4.33 - 4.90: 54470 Nonbonded interactions: 126604 Sorted by model distance: nonbonded pdb=" SG CYS E 22 " pdb=" SG CYS E 61 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS K 22 " pdb=" SG CYS K 61 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS G 22 " pdb=" SG CYS G 61 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS J 22 " pdb=" SG CYS J 61 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS B 22 " pdb=" SG CYS B 61 " model vdw 2.035 3.760 ... (remaining 126599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.410 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.044 15340 Z= 0.573 Angle : 0.935 6.325 20787 Z= 0.635 Chirality : 0.045 0.123 2431 Planarity : 0.007 0.096 2782 Dihedral : 12.312 83.894 5356 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 1.24 % Allowed : 8.70 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.36 (0.15), residues: 2093 helix: -3.87 (0.19), residues: 260 sheet: 0.11 (0.18), residues: 611 loop : -2.01 (0.13), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 89 PHE 0.002 0.000 PHE B 66 TYR 0.001 0.000 TYR E 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 595 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7822 (mm) cc_final: 0.7597 (mm) REVERT: C 53 ASP cc_start: 0.7610 (m-30) cc_final: 0.7305 (m-30) REVERT: C 91 ASP cc_start: 0.6961 (p0) cc_final: 0.6640 (p0) REVERT: C 101 THR cc_start: 0.7957 (p) cc_final: 0.7095 (t) REVERT: E 59 VAL cc_start: 0.7181 (m) cc_final: 0.6957 (p) REVERT: F 53 ASP cc_start: 0.7699 (m-30) cc_final: 0.7455 (m-30) REVERT: F 101 THR cc_start: 0.6753 (p) cc_final: 0.6329 (t) REVERT: G 52 MET cc_start: 0.7140 (mmm) cc_final: 0.6757 (tpp) REVERT: G 94 ASP cc_start: 0.7943 (t0) cc_final: 0.7741 (t70) REVERT: H 59 VAL cc_start: 0.8635 (m) cc_final: 0.8354 (p) REVERT: L 33 ILE cc_start: 0.7964 (mm) cc_final: 0.7614 (mm) REVERT: L 101 THR cc_start: 0.7563 (p) cc_final: 0.7345 (t) REVERT: L 126 ASP cc_start: 0.7016 (m-30) cc_final: 0.6755 (t70) REVERT: M 94 ASP cc_start: 0.7469 (t0) cc_final: 0.7062 (t0) outliers start: 0 outliers final: 0 residues processed: 595 average time/residue: 0.2810 time to fit residues: 241.0355 Evaluate side-chains 252 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 121 optimal weight: 50.0000 chunk 188 optimal weight: 30.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN E 70 ASN H 87 ASN I 31 GLN J 70 ASN K 70 ASN M 70 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15340 Z= 0.267 Angle : 0.717 11.051 20787 Z= 0.371 Chirality : 0.046 0.173 2431 Planarity : 0.004 0.029 2782 Dihedral : 6.798 76.577 2145 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.53 % Allowed : 13.59 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.26 (0.16), residues: 2093 helix: -2.06 (0.25), residues: 260 sheet: 0.20 (0.19), residues: 585 loop : -1.08 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 132 PHE 0.029 0.002 PHE E 158 TYR 0.013 0.002 TYR A 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 274 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8732 (mm) cc_final: 0.8292 (mm) REVERT: B 54 LEU cc_start: 0.8649 (tp) cc_final: 0.8448 (tt) REVERT: B 63 ILE cc_start: 0.8274 (pt) cc_final: 0.7814 (pt) REVERT: C 162 TYR cc_start: 0.7196 (m-80) cc_final: 0.6156 (m-10) REVERT: E 59 VAL cc_start: 0.8391 (m) cc_final: 0.8108 (t) REVERT: E 93 LEU cc_start: 0.8166 (tp) cc_final: 0.7794 (tp) REVERT: E 106 GLN cc_start: 0.7360 (mm110) cc_final: 0.7086 (mm-40) REVERT: F 34 ASP cc_start: 0.8530 (t0) cc_final: 0.8329 (t70) REVERT: F 52 MET cc_start: 0.7642 (mmm) cc_final: 0.7030 (mtt) REVERT: G 27 LYS cc_start: 0.7107 (mmmt) cc_final: 0.6784 (mmmm) REVERT: G 52 MET cc_start: 0.7512 (mmm) cc_final: 0.7141 (mmm) REVERT: H 13 PHE cc_start: 0.8316 (m-80) cc_final: 0.8021 (m-80) REVERT: I 126 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.5757 (t70) REVERT: L 40 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8490 (tttp) REVERT: M 126 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6679 (t0) REVERT: M 148 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8004 (p) outliers start: 73 outliers final: 35 residues processed: 322 average time/residue: 0.2735 time to fit residues: 129.2105 Evaluate side-chains 237 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 49 SER Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 20.0000 chunk 58 optimal weight: 30.0000 chunk 157 optimal weight: 30.0000 chunk 128 optimal weight: 50.0000 chunk 52 optimal weight: 30.0000 chunk 189 optimal weight: 20.0000 chunk 204 optimal weight: 5.9990 chunk 168 optimal weight: 30.0000 chunk 187 optimal weight: 20.0000 chunk 64 optimal weight: 30.0000 chunk 151 optimal weight: 30.0000 overall best weight: 19.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.9813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 15340 Z= 0.440 Angle : 0.769 8.569 20787 Z= 0.402 Chirality : 0.046 0.171 2431 Planarity : 0.004 0.033 2782 Dihedral : 7.345 78.694 2145 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.90 % Allowed : 15.01 % Favored : 80.09 % 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: -0.85 (0.17), residues: 2093 helix: -1.50 (0.27), residues: 260 sheet: 0.23 (0.21), residues: 585 loop : -0.71 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS M 132 PHE 0.031 0.002 PHE E 158 TYR 0.021 0.003 TYR K 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 204 time to evaluate : 1.646 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8394 (mt0) cc_final: 0.8113 (mt0) REVERT: B 149 GLU cc_start: 0.6544 (mt-10) cc_final: 0.6329 (mp0) REVERT: C 8 GLN cc_start: 0.7884 (mt0) cc_final: 0.7468 (mt0) REVERT: C 74 LYS cc_start: 0.8544 (tptt) cc_final: 0.8280 (mtmm) REVERT: C 128 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5259 (mt-10) REVERT: C 162 TYR cc_start: 0.8294 (m-80) cc_final: 0.7243 (m-10) REVERT: D 27 LYS cc_start: 0.7505 (mmtp) cc_final: 0.7287 (mmmm) REVERT: D 52 MET cc_start: 0.7470 (mmm) cc_final: 0.7039 (mtp) REVERT: G 27 LYS cc_start: 0.7483 (mmmt) cc_final: 0.6883 (mmmm) REVERT: G 52 MET cc_start: 0.8111 (mmm) cc_final: 0.7882 (mmt) REVERT: I 27 LYS cc_start: 0.8168 (mmpt) cc_final: 0.7309 (mmmm) REVERT: I 30 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7888 (p0) REVERT: K 149 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6794 (mm-30) REVERT: L 40 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8262 (ttmm) REVERT: M 27 LYS cc_start: 0.7809 (mmtp) cc_final: 0.7606 (mmmm) REVERT: M 157 ASN cc_start: 0.7750 (t0) cc_final: 0.7013 (t0) outliers start: 79 outliers final: 47 residues processed: 268 average time/residue: 0.2669 time to fit residues: 104.9459 Evaluate side-chains 201 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 151 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 152 PHE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 20.0000 chunk 142 optimal weight: 0.0170 chunk 98 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 189 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 99 optimal weight: 40.0000 chunk 179 optimal weight: 30.0000 chunk 54 optimal weight: 6.9990 overall best weight: 6.8030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 ASN J 129 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 1.0120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15340 Z= 0.206 Angle : 0.597 11.658 20787 Z= 0.302 Chirality : 0.044 0.136 2431 Planarity : 0.003 0.031 2782 Dihedral : 6.455 71.345 2145 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.54 % Allowed : 17.06 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.58 (0.17), residues: 2093 helix: -1.17 (0.27), residues: 273 sheet: 0.44 (0.21), residues: 585 loop : -0.57 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 132 PHE 0.024 0.002 PHE E 158 TYR 0.013 0.001 TYR K 162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 178 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.8622 (tp) cc_final: 0.8325 (tt) REVERT: B 149 GLU cc_start: 0.6206 (mt-10) cc_final: 0.5978 (mp0) REVERT: C 8 GLN cc_start: 0.7904 (mt0) cc_final: 0.7450 (mt0) REVERT: C 110 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7538 (tttt) REVERT: C 128 GLU cc_start: 0.5896 (OUTLIER) cc_final: 0.4962 (mp0) REVERT: D 27 LYS cc_start: 0.7703 (mmtp) cc_final: 0.7482 (mmmm) REVERT: D 152 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5224 (m-80) REVERT: G 52 MET cc_start: 0.8042 (mmm) cc_final: 0.7708 (mmt) REVERT: I 40 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8050 (ttmm) REVERT: I 52 MET cc_start: 0.7525 (mpp) cc_final: 0.7042 (mpp) REVERT: L 44 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8559 (tp30) REVERT: M 27 LYS cc_start: 0.7824 (mmtp) cc_final: 0.7622 (mmmm) outliers start: 57 outliers final: 32 residues processed: 216 average time/residue: 0.2348 time to fit residues: 77.9595 Evaluate side-chains 179 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 142 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain L residue 70 ASN Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 103 ILE Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 50.0000 chunk 114 optimal weight: 40.0000 chunk 2 optimal weight: 6.9990 chunk 149 optimal weight: 40.0000 chunk 82 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 138 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 102 optimal weight: 30.0000 chunk 180 optimal weight: 20.0000 chunk 50 optimal weight: 40.0000 overall best weight: 15.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 1.0674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15340 Z= 0.353 Angle : 0.670 9.774 20787 Z= 0.342 Chirality : 0.044 0.144 2431 Planarity : 0.003 0.031 2782 Dihedral : 6.618 67.384 2145 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.09 % Allowed : 17.06 % Favored : 78.85 % 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: -0.69 (0.17), residues: 2093 helix: -1.35 (0.32), residues: 182 sheet: 0.35 (0.21), residues: 585 loop : -0.69 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS M 132 PHE 0.023 0.002 PHE E 158 TYR 0.017 0.002 TYR K 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 135 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6339 (mp0) REVERT: C 8 GLN cc_start: 0.8011 (mt0) cc_final: 0.7467 (mt0) REVERT: C 30 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7798 (p0) REVERT: C 128 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.5836 (mp0) REVERT: D 152 PHE cc_start: 0.6484 (OUTLIER) cc_final: 0.5307 (m-80) REVERT: G 52 MET cc_start: 0.8033 (mmm) cc_final: 0.7625 (mmt) REVERT: H 40 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8422 (tttm) REVERT: I 40 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7773 (ttmp) REVERT: J 149 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6863 (tm-30) REVERT: M 149 GLU cc_start: 0.7329 (tm-30) cc_final: 0.7108 (tm-30) outliers start: 66 outliers final: 51 residues processed: 185 average time/residue: 0.2262 time to fit residues: 65.7719 Evaluate side-chains 177 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 121 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 152 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 118 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 167 optimal weight: 50.0000 chunk 93 optimal weight: 10.0000 chunk 16 optimal weight: 40.0000 chunk 66 optimal weight: 7.9990 chunk 105 optimal weight: 50.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN D 129 ASN E 129 ASN H 129 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 1.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15340 Z= 0.209 Angle : 0.595 11.445 20787 Z= 0.297 Chirality : 0.043 0.133 2431 Planarity : 0.003 0.030 2782 Dihedral : 6.137 66.941 2145 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.78 % Allowed : 19.04 % Favored : 77.17 % 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: -0.57 (0.17), residues: 2093 helix: -1.35 (0.32), residues: 182 sheet: 0.45 (0.21), residues: 585 loop : -0.61 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 132 PHE 0.020 0.002 PHE E 158 TYR 0.009 0.001 TYR K 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 148 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 LYS cc_start: 0.4540 (mptt) cc_final: 0.2158 (mmtt) REVERT: C 8 GLN cc_start: 0.8002 (mt0) cc_final: 0.7497 (mt0) REVERT: C 74 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7579 (mtmm) REVERT: D 152 PHE cc_start: 0.6266 (OUTLIER) cc_final: 0.5033 (m-80) REVERT: G 52 MET cc_start: 0.7979 (mmm) cc_final: 0.7541 (mmt) REVERT: I 40 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7819 (ttmp) REVERT: J 149 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6808 (tm-30) outliers start: 61 outliers final: 47 residues processed: 190 average time/residue: 0.2364 time to fit residues: 69.6892 Evaluate side-chains 178 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 128 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 152 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 0.3980 chunk 22 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 chunk 146 optimal weight: 50.0000 chunk 113 optimal weight: 20.0000 chunk 169 optimal weight: 40.0000 chunk 112 optimal weight: 30.0000 chunk 200 optimal weight: 30.0000 chunk 125 optimal weight: 30.0000 chunk 122 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 overall best weight: 9.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 1.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15340 Z= 0.249 Angle : 0.607 11.257 20787 Z= 0.303 Chirality : 0.043 0.135 2431 Planarity : 0.003 0.030 2782 Dihedral : 6.001 63.067 2145 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.09 % Allowed : 19.11 % Favored : 76.80 % 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: -0.59 (0.17), residues: 2093 helix: -1.33 (0.33), residues: 182 sheet: 0.43 (0.21), residues: 585 loop : -0.62 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 132 PHE 0.019 0.002 PHE D 152 TYR 0.010 0.001 TYR K 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 136 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 LYS cc_start: 0.4643 (mptt) cc_final: 0.2147 (mmtt) REVERT: C 74 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7670 (mtmm) REVERT: D 152 PHE cc_start: 0.6252 (OUTLIER) cc_final: 0.4955 (m-80) REVERT: H 40 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8485 (tttm) REVERT: H 110 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7827 (ttpp) REVERT: I 40 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7801 (ttmp) REVERT: J 149 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6863 (tm-30) REVERT: K 73 LYS cc_start: 0.6088 (mtpt) cc_final: 0.5855 (mmmm) REVERT: M 52 MET cc_start: 0.7370 (mmm) cc_final: 0.6506 (mtt) outliers start: 66 outliers final: 52 residues processed: 187 average time/residue: 0.2465 time to fit residues: 70.6134 Evaluate side-chains 173 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 116 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 152 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 118 GLU Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 119 optimal weight: 20.0000 chunk 60 optimal weight: 40.0000 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN F 70 ASN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 1.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15340 Z= 0.194 Angle : 0.598 16.784 20787 Z= 0.292 Chirality : 0.043 0.134 2431 Planarity : 0.003 0.029 2782 Dihedral : 5.785 64.368 2145 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.47 % Allowed : 20.22 % Favored : 76.30 % 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: -0.51 (0.17), residues: 2093 helix: -1.29 (0.33), residues: 182 sheet: 0.51 (0.22), residues: 585 loop : -0.57 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 132 PHE 0.019 0.001 PHE D 152 TYR 0.006 0.001 TYR K 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 126 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 LYS cc_start: 0.4612 (mptt) cc_final: 0.2177 (mmtt) REVERT: C 74 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7759 (mtmm) REVERT: D 152 PHE cc_start: 0.6166 (OUTLIER) cc_final: 0.4790 (m-80) REVERT: H 40 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8509 (tttm) REVERT: H 110 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7777 (ttpp) REVERT: I 40 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7731 (tttp) REVERT: I 52 MET cc_start: 0.7277 (mpp) cc_final: 0.6709 (mpp) REVERT: J 149 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6891 (tm-30) REVERT: M 52 MET cc_start: 0.7338 (mmm) cc_final: 0.6566 (mtt) outliers start: 56 outliers final: 46 residues processed: 169 average time/residue: 0.2350 time to fit residues: 62.0681 Evaluate side-chains 166 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 115 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 152 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 118 GLU Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 40.0000 chunk 192 optimal weight: 60.0000 chunk 175 optimal weight: 30.0000 chunk 186 optimal weight: 50.0000 chunk 112 optimal weight: 40.0000 chunk 81 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 chunk 57 optimal weight: 50.0000 chunk 168 optimal weight: 6.9990 chunk 176 optimal weight: 50.0000 chunk 122 optimal weight: 40.0000 overall best weight: 18.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 1.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15340 Z= 0.418 Angle : 0.716 18.307 20787 Z= 0.362 Chirality : 0.045 0.155 2431 Planarity : 0.004 0.034 2782 Dihedral : 6.452 62.869 2145 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.09 % Allowed : 19.98 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.77 (0.17), residues: 2093 helix: -1.52 (0.32), residues: 182 sheet: 0.54 (0.22), residues: 559 loop : -0.83 (0.15), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 89 PHE 0.025 0.002 PHE M 158 TYR 0.014 0.002 TYR K 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 116 time to evaluate : 1.828 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8529 (tt0) cc_final: 0.8296 (tm-30) REVERT: D 152 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.5051 (m-80) REVERT: H 40 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8431 (tttm) REVERT: H 110 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7674 (ttpp) REVERT: I 40 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7887 (ttmp) REVERT: J 149 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7074 (tm-30) REVERT: M 52 MET cc_start: 0.7462 (mmm) cc_final: 0.6870 (mtt) outliers start: 66 outliers final: 58 residues processed: 170 average time/residue: 0.2426 time to fit residues: 64.6185 Evaluate side-chains 167 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 105 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 152 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 118 GLU Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 30.0000 chunk 120 optimal weight: 4.9990 chunk 93 optimal weight: 30.0000 chunk 137 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 190 optimal weight: 30.0000 chunk 165 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 ASN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 1.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15340 Z= 0.223 Angle : 0.629 18.231 20787 Z= 0.308 Chirality : 0.044 0.144 2431 Planarity : 0.003 0.039 2782 Dihedral : 5.980 63.773 2145 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.10 % Allowed : 21.71 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.62 (0.17), residues: 2093 helix: -1.43 (0.33), residues: 182 sheet: 0.50 (0.21), residues: 637 loop : -0.73 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 132 PHE 0.025 0.002 PHE M 158 TYR 0.010 0.001 TYR I 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 122 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 LYS cc_start: 0.4617 (mptt) cc_final: 0.2266 (mmtt) REVERT: B 57 GLU cc_start: 0.8421 (tt0) cc_final: 0.8167 (tm-30) REVERT: C 74 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7747 (mtmm) REVERT: D 152 PHE cc_start: 0.6291 (OUTLIER) cc_final: 0.4859 (m-80) REVERT: H 40 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8537 (tttm) REVERT: H 110 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7811 (ttpp) REVERT: I 40 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7803 (ttmp) REVERT: I 52 MET cc_start: 0.7310 (mpp) cc_final: 0.6872 (mpp) REVERT: J 149 GLU cc_start: 0.7351 (tm-30) cc_final: 0.7045 (tm-30) REVERT: M 52 MET cc_start: 0.7403 (mmm) cc_final: 0.6730 (mtt) outliers start: 50 outliers final: 45 residues processed: 161 average time/residue: 0.2240 time to fit residues: 57.4593 Evaluate side-chains 163 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 113 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 152 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 118 GLU Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 50.0000 chunk 50 optimal weight: 0.0870 chunk 152 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 169 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 145 optimal weight: 30.0000 overall best weight: 7.7968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 163 GLN F 8 GLN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.058670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.049456 restraints weight = 71864.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.050841 restraints weight = 42604.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.051710 restraints weight = 29025.153| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 1.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15340 Z= 0.221 Angle : 0.621 18.181 20787 Z= 0.304 Chirality : 0.044 0.190 2431 Planarity : 0.003 0.037 2782 Dihedral : 5.839 62.667 2145 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.47 % Allowed : 21.40 % Favored : 75.12 % 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: -0.57 (0.17), residues: 2093 helix: -1.35 (0.34), residues: 182 sheet: 0.51 (0.21), residues: 637 loop : -0.67 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 132 PHE 0.027 0.002 PHE M 158 TYR 0.009 0.001 TYR D 162 =============================================================================== Job complete usr+sys time: 2473.72 seconds wall clock time: 46 minutes 25.63 seconds (2785.63 seconds total)