Starting phenix.real_space_refine on Sat Mar 16 16:59:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/03_2024/5flu_3222.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/03_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_3222/03_2024/5flu_3222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/03_2024/5flu_3222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/03_2024/5flu_3222.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/03_2024/5flu_3222.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15132 Number of models: 1 Model: "" Number of chains: 13 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} Chain: "B" 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} Chain: "C" 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} Chain: "D" 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} Chain: "E" 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} Chain: "F" 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} Chain: "G" 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} Chain: "H" 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} Chain: "I" 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} Chain: "J" 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} Chain: "K" 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} Chain: "L" 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} Chain: "M" 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} Time building chain proxies: 7.29, per 1000 atoms: 0.48 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=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 61 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 61 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 61 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 61 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 61 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 61 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 61 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 61 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 61 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.15 Conformation dependent library (CDL) restraints added in 2.7 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: 1.95 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: 4.50 Time building geometry restraints manager: 5.62 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: 99.72 - 106.03: 273 106.03 - 112.34: 8306 112.34 - 118.64: 4062 118.64 - 124.95: 8082 124.95 - 131.26: 64 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: 279 33.56 - 50.34: 26 50.34 - 67.12: 52 67.12 - 83.89: 65 Dihedral angle restraints: 9061 sinusoidal: 3263 harmonic: 5798 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 61 " pdb=" CB CYS E 61 " ideal model delta sinusoidal sigma weight residual -86.00 -54.93 -31.07 1 1.00e+01 1.00e-02 1.38e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 61 " pdb=" CB CYS J 61 " ideal model delta sinusoidal sigma weight residual -86.00 -54.94 -31.06 1 1.00e+01 1.00e-02 1.38e+01 dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 61 " pdb=" CB CYS M 61 " ideal model delta sinusoidal sigma weight residual -86.00 -54.96 -31.04 1 1.00e+01 1.00e-02 1.37e+01 ... (remaining 9058 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: 2.21 - 2.75: 1545 2.75 - 3.29: 16056 3.29 - 3.83: 25346 3.83 - 4.36: 31495 4.36 - 4.90: 52126 Nonbonded interactions: 126568 Sorted by model distance: nonbonded pdb=" O HIS M 89 " pdb=" OG SER M 90 " model vdw 2.213 2.440 nonbonded pdb=" O HIS K 89 " pdb=" OG SER K 90 " model vdw 2.213 2.440 nonbonded pdb=" O HIS F 89 " pdb=" OG SER F 90 " model vdw 2.213 2.440 nonbonded pdb=" O HIS C 89 " pdb=" OG SER C 90 " model vdw 2.213 2.440 nonbonded pdb=" O HIS D 89 " pdb=" OG SER D 90 " model vdw 2.214 2.440 ... (remaining 126563 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.020 Extract box with map and model: 1.260 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 38.910 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.090 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.610 ------------------------------------------------------------------------------- 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= 0.569 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 : 2.213 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 : 1.589 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: 0.2647 time to fit residues: 226.1306 Evaluate side-chains 252 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.750 ------------------------------------------------------------------------------- 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: 9.9990 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 163 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 121 optimal weight: 50.0000 chunk 188 optimal weight: 7.9990 overall best weight: 6.3188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15340 Z= 0.233 Angle : 0.665 10.222 20787 Z= 0.344 Chirality : 0.046 0.173 2431 Planarity : 0.004 0.039 2782 Dihedral : 6.913 84.562 2145 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.16 % Allowed : 14.08 % Favored : 81.76 % 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: -1.14 (0.16), residues: 2093 helix: -1.95 (0.26), residues: 260 sheet: 0.30 (0.19), residues: 585 loop : -1.01 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 89 PHE 0.028 0.002 PHE H 158 TYR 0.017 0.002 TYR H 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 348 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 281 time to evaluate : 1.638 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: 0.8664 (mm) cc_final: 0.8186 (mm) REVERT: A 52 MET cc_start: 0.7078 (mmm) cc_final: 0.6714 (mtp) REVERT: B 114 PHE cc_start: 0.8105 (m-80) cc_final: 0.7895 (m-80) REVERT: C 162 TYR cc_start: 0.6477 (m-80) cc_final: 0.6122 (m-10) REVERT: D 52 MET cc_start: 0.7163 (mmm) cc_final: 0.6955 (mmm) REVERT: E 85 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8603 (mt) REVERT: E 106 GLN cc_start: 0.7209 (mm110) cc_final: 0.6956 (mm-40) REVERT: F 34 ASP cc_start: 0.8279 (t0) cc_final: 0.7988 (t70) REVERT: F 52 MET cc_start: 0.7512 (mmm) cc_final: 0.6791 (mtt) REVERT: F 110 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8172 (mmmm) REVERT: G 27 LYS cc_start: 0.7061 (mmmt) cc_final: 0.6617 (mmmm) REVERT: G 52 MET cc_start: 0.7240 (mmm) cc_final: 0.6873 (mpp) REVERT: H 110 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7301 (mtpp) REVERT: I 148 THR cc_start: 0.8072 (m) cc_final: 0.7818 (p) REVERT: M 94 ASP cc_start: 0.7821 (t0) cc_final: 0.7487 (t0) REVERT: M 148 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7897 (p) outliers start: 67 outliers final: 37 residues processed: 327 average time/residue: 0.2618 time to fit residues: 125.5944 Evaluate side-chains 258 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 85 ILE 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 110 LYS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 53 ASP 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 85 ILE Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 110 LYS 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 H residue 155 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 31 GLN Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 44 GLU 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 112 VAL Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain M residue 53 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: 30.0000 chunk 58 optimal weight: 40.0000 chunk 157 optimal weight: 10.0000 chunk 128 optimal weight: 50.0000 chunk 52 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 204 optimal weight: 50.0000 chunk 168 optimal weight: 30.0000 chunk 187 optimal weight: 40.0000 chunk 64 optimal weight: 40.0000 chunk 151 optimal weight: 30.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 106 GLN G 70 ASN I 8 GLN J 31 GLN J 106 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.9945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 15340 Z= 0.451 Angle : 0.790 9.340 20787 Z= 0.415 Chirality : 0.046 0.180 2431 Planarity : 0.004 0.030 2782 Dihedral : 7.394 84.966 2145 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 5.71 % Allowed : 14.33 % Favored : 79.96 % 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: -0.81 (0.17), residues: 2093 helix: -1.72 (0.26), residues: 260 sheet: 0.49 (0.21), residues: 559 loop : -0.73 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 89 PHE 0.032 0.003 PHE E 158 TYR 0.019 0.003 TYR M 133 *********************** 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 304 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 212 time to evaluate : 1.649 Fit side-chains revert: symmetry clash REVERT: B 149 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6368 (mp0) REVERT: C 8 GLN cc_start: 0.7736 (mt0) cc_final: 0.7283 (mt0) REVERT: C 52 MET cc_start: 0.7580 (mpp) cc_final: 0.7368 (mmt) REVERT: C 74 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.6884 (mmmt) REVERT: G 8 GLN cc_start: 0.8205 (mt0) cc_final: 0.7742 (mt0) REVERT: G 27 LYS cc_start: 0.7452 (mmmt) cc_final: 0.6908 (mmmm) REVERT: G 52 MET cc_start: 0.7996 (mmm) cc_final: 0.7675 (mmt) REVERT: G 54 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8499 (mm) REVERT: H 162 TYR cc_start: 0.7953 (m-80) cc_final: 0.7703 (m-80) REVERT: I 27 LYS cc_start: 0.7978 (mmpt) cc_final: 0.7227 (mmmm) REVERT: I 52 MET cc_start: 0.7742 (mpp) cc_final: 0.7468 (mpp) REVERT: J 74 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7607 (mptt) REVERT: J 128 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7338 (mm-30) REVERT: K 149 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6886 (mm-30) REVERT: L 149 GLU cc_start: 0.7970 (pm20) cc_final: 0.6965 (pp20) REVERT: M 54 LEU cc_start: 0.8683 (mp) cc_final: 0.8420 (tt) outliers start: 92 outliers final: 49 residues processed: 287 average time/residue: 0.2615 time to fit residues: 110.8926 Evaluate side-chains 203 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 151 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 152 PHE 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 106 GLN Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 85 ILE 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 17 VAL Chi-restraints excluded: chain H residue 105 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 152 PHE Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 74 LYS 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 43 LEU Chi-restraints excluded: chain M residue 112 VAL 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: 7.9990 chunk 142 optimal weight: 50.0000 chunk 98 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 189 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 179 optimal weight: 30.0000 chunk 54 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 70 ASN K 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 1.0137 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= 0.199 Angle : 0.587 10.335 20787 Z= 0.296 Chirality : 0.043 0.141 2431 Planarity : 0.003 0.022 2782 Dihedral : 6.346 76.624 2145 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.72 % Allowed : 16.69 % Favored : 79.59 % 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: -0.52 (0.17), residues: 2093 helix: -1.28 (0.28), residues: 260 sheet: 0.46 (0.21), residues: 585 loop : -0.49 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 132 PHE 0.025 0.002 PHE E 158 TYR 0.009 0.001 TYR M 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 256 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 196 time to evaluate : 1.638 Fit side-chains revert: symmetry clash REVERT: C 8 GLN cc_start: 0.7790 (mt0) cc_final: 0.7470 (mt0) REVERT: C 52 MET cc_start: 0.7787 (mpp) cc_final: 0.7577 (mmt) REVERT: C 74 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7519 (mtmm) REVERT: C 110 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7600 (tttt) REVERT: C 162 TYR cc_start: 0.7775 (m-80) cc_final: 0.6700 (m-10) REVERT: G 8 GLN cc_start: 0.8232 (mt0) cc_final: 0.7937 (mt0) REVERT: G 149 GLU cc_start: 0.7935 (pm20) cc_final: 0.7489 (tm-30) REVERT: H 67 LYS cc_start: 0.6907 (pttp) cc_final: 0.6551 (tmmt) REVERT: H 92 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7152 (mt-10) REVERT: I 54 LEU cc_start: 0.8772 (mm) cc_final: 0.8491 (mm) REVERT: J 128 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7281 (mm-30) REVERT: K 74 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7767 (mmtm) REVERT: L 149 GLU cc_start: 0.7834 (pm20) cc_final: 0.7105 (pp20) outliers start: 60 outliers final: 37 residues processed: 239 average time/residue: 0.2365 time to fit residues: 86.4456 Evaluate side-chains 189 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 16 THR 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 C residue 24 ILE 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 112 VAL Chi-restraints excluded: chain C residue 128 GLU 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 17 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 152 PHE 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 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 44 GLU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 106 GLN Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 134 THR 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: 7.9990 chunk 114 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 chunk 149 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 171 optimal weight: 20.0000 chunk 138 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 102 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 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: 0.7905 moved from start: 1.0385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15340 Z= 0.202 Angle : 0.572 11.706 20787 Z= 0.287 Chirality : 0.043 0.128 2431 Planarity : 0.003 0.023 2782 Dihedral : 6.090 68.552 2145 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.35 % Allowed : 17.80 % 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: -0.20 (0.17), residues: 2093 helix: -1.18 (0.29), residues: 260 sheet: 1.08 (0.22), residues: 546 loop : -0.42 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 132 PHE 0.022 0.002 PHE E 158 TYR 0.009 0.001 TYR F 133 *********************** 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 222 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 168 time to evaluate : 1.622 Fit side-chains REVERT: C 8 GLN cc_start: 0.7805 (mt0) cc_final: 0.7262 (mt0) REVERT: C 52 MET cc_start: 0.7742 (mpp) cc_final: 0.7465 (mmt) REVERT: C 74 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7598 (mtmm) REVERT: C 110 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7601 (tttt) REVERT: C 162 TYR cc_start: 0.7979 (m-80) cc_final: 0.7069 (m-10) REVERT: D 152 PHE cc_start: 0.6181 (OUTLIER) cc_final: 0.5143 (m-80) REVERT: G 8 GLN cc_start: 0.8265 (mt0) cc_final: 0.7998 (mt0) REVERT: H 67 LYS cc_start: 0.6929 (pttp) cc_final: 0.6651 (tmmt) REVERT: H 92 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7261 (mt-10) REVERT: I 40 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8245 (ttmt) REVERT: I 52 MET cc_start: 0.7373 (mpp) cc_final: 0.6804 (mpp) REVERT: J 128 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7206 (mm-30) REVERT: K 74 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7815 (mmtp) REVERT: L 149 GLU cc_start: 0.7840 (pm20) cc_final: 0.7290 (pp20) REVERT: M 149 GLU cc_start: 0.7292 (tm-30) cc_final: 0.7048 (tm-30) outliers start: 54 outliers final: 39 residues processed: 206 average time/residue: 0.2225 time to fit residues: 71.8257 Evaluate side-chains 196 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 152 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 16 THR 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 74 LYS Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 128 GLU 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 110 LYS Chi-restraints excluded: chain E residue 152 PHE 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 17 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain H residue 4 ILE 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 33 ILE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 106 GLN Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 155 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 20.0000 chunk 181 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 118 optimal weight: 30.0000 chunk 49 optimal weight: 8.9990 chunk 201 optimal weight: 30.0000 chunk 167 optimal weight: 30.0000 chunk 93 optimal weight: 8.9990 chunk 16 optimal weight: 40.0000 chunk 66 optimal weight: 10.0000 chunk 105 optimal weight: 50.0000 overall best weight: 13.5996 ------------------------------------------------------------------------------- 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** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 1.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15340 Z= 0.313 Angle : 0.625 11.902 20787 Z= 0.318 Chirality : 0.043 0.140 2431 Planarity : 0.003 0.024 2782 Dihedral : 6.226 68.648 2145 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.22 % Allowed : 18.11 % Favored : 77.67 % 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: -0.35 (0.17), residues: 2093 helix: -1.27 (0.28), residues: 260 sheet: 0.82 (0.22), residues: 559 loop : -0.45 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 132 PHE 0.021 0.002 PHE E 158 TYR 0.014 0.001 TYR E 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 211 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 143 time to evaluate : 1.701 Fit side-chains revert: symmetry clash REVERT: C 8 GLN cc_start: 0.7857 (mt0) cc_final: 0.7408 (mt0) REVERT: C 52 MET cc_start: 0.7781 (mpp) cc_final: 0.7519 (mmm) REVERT: D 152 PHE cc_start: 0.6368 (OUTLIER) cc_final: 0.5201 (m-80) REVERT: G 54 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8239 (mm) REVERT: H 110 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7466 (ttpp) REVERT: I 40 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8222 (ttmt) REVERT: I 52 MET cc_start: 0.7294 (mpp) cc_final: 0.6745 (mpp) REVERT: J 74 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7513 (mptt) REVERT: L 149 GLU cc_start: 0.8020 (pm20) cc_final: 0.7535 (pp20) outliers start: 68 outliers final: 52 residues processed: 194 average time/residue: 0.2295 time to fit residues: 69.9924 Evaluate side-chains 180 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 123 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 16 THR 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 112 VAL Chi-restraints excluded: chain C residue 128 GLU 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 110 LYS Chi-restraints excluded: chain E residue 152 PHE 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 17 VAL Chi-restraints excluded: chain G residue 54 LEU 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 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 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 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 44 GLU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 106 GLN 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 152 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 2.9990 chunk 22 optimal weight: 50.0000 chunk 114 optimal weight: 30.0000 chunk 146 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 169 optimal weight: 40.0000 chunk 112 optimal weight: 30.0000 chunk 200 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 92 optimal weight: 50.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 1.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15340 Z= 0.195 Angle : 0.566 12.922 20787 Z= 0.282 Chirality : 0.043 0.134 2431 Planarity : 0.003 0.026 2782 Dihedral : 5.772 62.626 2145 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.60 % Allowed : 19.04 % Favored : 77.36 % 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: -0.16 (0.17), residues: 2093 helix: -1.23 (0.28), residues: 260 sheet: 1.15 (0.22), residues: 546 loop : -0.40 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 132 PHE 0.019 0.001 PHE E 158 TYR 0.010 0.001 TYR E 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 206 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 148 time to evaluate : 1.690 Fit side-chains revert: symmetry clash REVERT: C 52 MET cc_start: 0.7697 (mpp) cc_final: 0.7435 (mmm) REVERT: C 74 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7512 (mtmm) REVERT: D 152 PHE cc_start: 0.6342 (OUTLIER) cc_final: 0.5150 (m-80) REVERT: F 52 MET cc_start: 0.7819 (mmm) cc_final: 0.7541 (mmt) REVERT: H 110 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7508 (ttpp) REVERT: I 52 MET cc_start: 0.7166 (mpp) cc_final: 0.6583 (mpp) REVERT: L 149 GLU cc_start: 0.7874 (pm20) cc_final: 0.7543 (pp20) outliers start: 58 outliers final: 45 residues processed: 187 average time/residue: 0.2151 time to fit residues: 64.2435 Evaluate side-chains 177 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 129 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 16 THR 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 112 VAL Chi-restraints excluded: chain C residue 124 LEU 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 79 LEU 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 F residue 152 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain H residue 4 ILE 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 33 ILE Chi-restraints excluded: chain I residue 54 LEU 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 44 GLU Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 106 GLN Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 66 PHE 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 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: 50.0000 chunk 80 optimal weight: 0.4980 chunk 119 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 50.0000 chunk 38 optimal weight: 50.0000 chunk 127 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 99 optimal weight: 50.0000 chunk 18 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 overall best weight: 8.4990 ------------------------------------------------------------------------------- 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 8 GLN F 8 GLN G 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 1.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 15340 Z= 0.224 Angle : 0.595 13.145 20787 Z= 0.294 Chirality : 0.043 0.214 2431 Planarity : 0.003 0.024 2782 Dihedral : 5.805 65.298 2145 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.16 % Allowed : 18.86 % Favored : 76.99 % 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: -0.20 (0.18), residues: 2093 helix: -1.20 (0.29), residues: 260 sheet: 0.98 (0.22), residues: 559 loop : -0.38 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 132 PHE 0.019 0.002 PHE E 158 TYR 0.010 0.001 TYR E 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 202 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 135 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.8581 (tp) cc_final: 0.8365 (tt) REVERT: C 52 MET cc_start: 0.7634 (mpp) cc_final: 0.7327 (mmm) REVERT: D 152 PHE cc_start: 0.6199 (OUTLIER) cc_final: 0.5088 (m-80) REVERT: F 52 MET cc_start: 0.7763 (mmm) cc_final: 0.7518 (mmt) REVERT: H 110 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7437 (ttpp) REVERT: I 52 MET cc_start: 0.7231 (mpp) cc_final: 0.6707 (mpp) REVERT: L 149 GLU cc_start: 0.7865 (pm20) cc_final: 0.7519 (pp20) REVERT: M 52 MET cc_start: 0.7298 (mmm) cc_final: 0.7057 (mtt) outliers start: 67 outliers final: 53 residues processed: 187 average time/residue: 0.2158 time to fit residues: 64.3853 Evaluate side-chains 184 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 129 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 16 THR 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 112 VAL Chi-restraints excluded: chain C residue 124 LEU 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 110 LYS Chi-restraints excluded: chain E residue 152 PHE 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 17 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 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 11 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 54 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 44 GLU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 106 GLN 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 66 PHE Chi-restraints excluded: chain K residue 70 ASN 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 82 THR 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: 4.9990 chunk 192 optimal weight: 90.0000 chunk 175 optimal weight: 20.0000 chunk 186 optimal weight: 30.0000 chunk 112 optimal weight: 40.0000 chunk 81 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 57 optimal weight: 50.0000 chunk 168 optimal weight: 0.1980 chunk 176 optimal weight: 50.0000 chunk 122 optimal weight: 30.0000 overall best weight: 11.0394 ------------------------------------------------------------------------------- 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** ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 1.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 15340 Z= 0.267 Angle : 0.621 13.358 20787 Z= 0.309 Chirality : 0.043 0.196 2431 Planarity : 0.003 0.026 2782 Dihedral : 5.995 70.844 2145 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.97 % Allowed : 19.67 % Favored : 76.36 % 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: -0.14 (0.18), residues: 2093 helix: -1.20 (0.29), residues: 260 sheet: 1.07 (0.21), residues: 611 loop : -0.41 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 132 PHE 0.019 0.002 PHE E 158 TYR 0.010 0.001 TYR E 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 193 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 129 time to evaluate : 1.700 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7518 (tm-30) REVERT: C 52 MET cc_start: 0.7643 (mpp) cc_final: 0.7311 (mmm) REVERT: C 74 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7404 (mptt) REVERT: D 152 PHE cc_start: 0.6257 (OUTLIER) cc_final: 0.4995 (m-80) REVERT: F 52 MET cc_start: 0.7785 (mmm) cc_final: 0.7410 (mmt) REVERT: H 110 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7569 (ttpp) REVERT: I 52 MET cc_start: 0.7190 (mpp) cc_final: 0.6582 (mpp) REVERT: L 149 GLU cc_start: 0.7934 (pm20) cc_final: 0.7510 (pp20) outliers start: 64 outliers final: 56 residues processed: 180 average time/residue: 0.2140 time to fit residues: 61.7737 Evaluate side-chains 180 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 121 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 58 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 30 ASP 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 124 LEU 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 16 THR 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 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 17 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 110 LYS 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 11 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 54 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 44 GLU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 106 GLN 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 66 PHE Chi-restraints excluded: chain K residue 70 ASN 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 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: 6.9990 chunk 120 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 137 optimal weight: 30.0000 chunk 207 optimal weight: 9.9990 chunk 190 optimal weight: 0.0000 chunk 165 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 127 optimal weight: 40.0000 chunk 101 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 overall best weight: 5.3992 ------------------------------------------------------------------------------- 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** ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 1.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15340 Z= 0.177 Angle : 0.585 13.665 20787 Z= 0.286 Chirality : 0.043 0.175 2431 Planarity : 0.003 0.022 2782 Dihedral : 5.633 66.635 2145 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.98 % Allowed : 20.84 % Favored : 76.18 % 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: -0.10 (0.17), residues: 2093 helix: -1.15 (0.29), residues: 260 sheet: 1.26 (0.22), residues: 546 loop : -0.41 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 132 PHE 0.019 0.001 PHE D 152 TYR 0.008 0.001 TYR E 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 192 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 144 time to evaluate : 1.673 Fit side-chains revert: symmetry clash REVERT: C 52 MET cc_start: 0.7628 (mpp) cc_final: 0.7297 (mmt) REVERT: C 74 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7714 (mtmm) REVERT: D 152 PHE cc_start: 0.6240 (OUTLIER) cc_final: 0.5031 (m-80) REVERT: H 110 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7355 (ttpp) REVERT: L 149 GLU cc_start: 0.7827 (pm20) cc_final: 0.7607 (pp20) REVERT: M 52 MET cc_start: 0.7373 (mmm) cc_final: 0.6455 (mtt) outliers start: 48 outliers final: 43 residues processed: 177 average time/residue: 0.2187 time to fit residues: 61.9335 Evaluate side-chains 175 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 129 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR 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 74 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 124 LEU 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 17 VAL 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 F residue 112 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 152 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain H residue 4 ILE 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 H residue 160 LEU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 54 LEU 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 44 GLU Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 106 GLN Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 66 PHE 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 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: 30.0000 chunk 50 optimal weight: 50.0000 chunk 152 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 165 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 169 optimal weight: 30.0000 chunk 20 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 145 optimal weight: 8.9990 overall best weight: 9.7992 ------------------------------------------------------------------------------- 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** E 163 GLN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.050412 restraints weight = 71628.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.051835 restraints weight = 41163.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052702 restraints weight = 27134.042| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 1.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15340 Z= 0.244 Angle : 0.612 13.633 20787 Z= 0.302 Chirality : 0.043 0.187 2431 Planarity : 0.003 0.025 2782 Dihedral : 5.824 66.146 2145 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.78 % Allowed : 19.85 % Favored : 76.36 % 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: -0.06 (0.18), residues: 2093 helix: -1.15 (0.29), residues: 260 sheet: 1.15 (0.21), residues: 611 loop : -0.38 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 132 PHE 0.018 0.002 PHE E 158 TYR 0.008 0.001 TYR I 162 =============================================================================== Job complete usr+sys time: 2477.17 seconds wall clock time: 46 minutes 43.41 seconds (2803.41 seconds total)