Starting phenix.real_space_refine (version: dev) on Tue Feb 21 15:34:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/02_2023/5flu_3222.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/02_2023/5flu_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_3222/02_2023/5flu_3222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/02_2023/5flu_3222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/02_2023/5flu_3222.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flu_3222/02_2023/5flu_3222.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 8.46, per 1000 atoms: 0.56 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: 5.92 Conformation dependent library (CDL) restraints added in 2.5 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: 0.95 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: 4.48 Time building geometry restraints manager: 6.41 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.780 Check model and map are aligned: 0.220 Process input model: 40.560 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 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 % 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 *********************** 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 : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 595 average time/residue: 0.2822 time to fit residues: 240.0413 Evaluate side-chains 247 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.932 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3067 ------------------------------------------------------------------------------- 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: 5.9990 chunk 87 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 121 optimal weight: 50.0000 chunk 188 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 M 70 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.6028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 15340 Z= 0.285 Angle : 0.699 9.998 20787 Z= 0.367 Chirality : 0.047 0.187 2431 Planarity : 0.004 0.039 2782 Dihedral : 6.933 83.309 2145 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 4.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2093 helix: -2.01 (0.25), residues: 260 sheet: 0.24 (0.19), residues: 585 loop : -1.03 (0.16), residues: 1248 *********************** 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 341 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 265 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 38 residues processed: 316 average time/residue: 0.2802 time to fit residues: 128.5514 Evaluate side-chains 242 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 1.870 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.1736 time to fit residues: 13.4361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 20.0000 chunk 58 optimal weight: 50.0000 chunk 157 optimal weight: 5.9990 chunk 128 optimal weight: 50.0000 chunk 52 optimal weight: 30.0000 chunk 189 optimal weight: 8.9990 chunk 204 optimal weight: 40.0000 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: 18.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.9589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 15340 Z= 0.428 Angle : 0.756 8.362 20787 Z= 0.396 Chirality : 0.045 0.165 2431 Planarity : 0.004 0.029 2782 Dihedral : 7.446 86.052 2145 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.74 (0.17), residues: 2093 helix: -1.65 (0.27), residues: 260 sheet: 0.63 (0.21), residues: 559 loop : -0.74 (0.16), residues: 1274 *********************** 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 268 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 209 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 37 residues processed: 258 average time/residue: 0.2761 time to fit residues: 105.3756 Evaluate side-chains 177 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 1.727 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1716 time to fit residues: 13.2209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 30.0000 chunk 142 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 20 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 chunk 127 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 201 optimal weight: 20.0000 chunk 99 optimal weight: 40.0000 chunk 179 optimal weight: 20.0000 chunk 54 optimal weight: 30.0000 overall best weight: 11.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 GLN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN J 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 1.0158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 15340 Z= 0.278 Angle : 0.623 10.016 20787 Z= 0.315 Chirality : 0.043 0.141 2431 Planarity : 0.003 0.025 2782 Dihedral : 6.597 71.026 2145 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.17), residues: 2093 helix: -1.26 (0.28), residues: 260 sheet: 0.76 (0.21), residues: 559 loop : -0.61 (0.16), residues: 1274 *********************** 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 205 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 18 residues processed: 196 average time/residue: 0.2507 time to fit residues: 75.0832 Evaluate side-chains 157 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1783 time to fit residues: 7.6872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 30.0000 chunk 114 optimal weight: 40.0000 chunk 2 optimal weight: 0.7980 chunk 149 optimal weight: 20.0000 chunk 82 optimal weight: 0.0470 chunk 171 optimal weight: 40.0000 chunk 138 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 102 optimal weight: 50.0000 chunk 180 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 overall best weight: 7.7688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 GLN G 70 ASN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 1.0399 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= 0.214 Angle : 0.585 11.727 20787 Z= 0.293 Chirality : 0.043 0.134 2431 Planarity : 0.003 0.031 2782 Dihedral : 6.191 68.564 2145 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.17), residues: 2093 helix: -1.10 (0.29), residues: 260 sheet: 0.90 (0.22), residues: 559 loop : -0.49 (0.16), residues: 1274 *********************** 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 182 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 174 average time/residue: 0.2436 time to fit residues: 65.9048 Evaluate side-chains 151 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 1.706 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1553 time to fit residues: 4.7122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 39 optimal weight: 50.0000 chunk 118 optimal weight: 40.0000 chunk 49 optimal weight: 8.9990 chunk 201 optimal weight: 20.0000 chunk 167 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 16 optimal weight: 40.0000 chunk 66 optimal weight: 20.0000 chunk 105 optimal weight: 40.0000 overall best weight: 10.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** 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: 0.7939 moved from start: 1.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 15340 Z= 0.264 Angle : 0.608 11.805 20787 Z= 0.308 Chirality : 0.043 0.132 2431 Planarity : 0.003 0.032 2782 Dihedral : 6.132 66.658 2145 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 1.67 % 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: -0.28 (0.17), residues: 2093 helix: -1.06 (0.29), residues: 260 sheet: 1.04 (0.22), residues: 533 loop : -0.51 (0.16), residues: 1300 *********************** 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 167 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 20 residues processed: 159 average time/residue: 0.2216 time to fit residues: 56.8786 Evaluate side-chains 145 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.869 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1616 time to fit residues: 8.0392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 114 optimal weight: 50.0000 chunk 146 optimal weight: 30.0000 chunk 113 optimal weight: 7.9990 chunk 169 optimal weight: 30.0000 chunk 112 optimal weight: 30.0000 chunk 200 optimal weight: 0.0870 chunk 125 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 92 optimal weight: 30.0000 overall best weight: 7.0168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** 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: 0.7918 moved from start: 1.0836 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= 0.199 Angle : 0.576 13.021 20787 Z= 0.285 Chirality : 0.043 0.140 2431 Planarity : 0.003 0.033 2782 Dihedral : 5.849 64.347 2145 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 0.87 % 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: -0.23 (0.17), residues: 2093 helix: -1.05 (0.28), residues: 260 sheet: 0.96 (0.22), residues: 559 loop : -0.44 (0.16), residues: 1274 *********************** 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 158 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 13 residues processed: 154 average time/residue: 0.2254 time to fit residues: 55.1730 Evaluate side-chains 139 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 1.639 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1475 time to fit residues: 5.8220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 119 optimal weight: 8.9990 chunk 60 optimal weight: 0.4980 chunk 39 optimal weight: 50.0000 chunk 38 optimal weight: 40.0000 chunk 127 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 99 optimal weight: 40.0000 chunk 18 optimal weight: 20.0000 chunk 157 optimal weight: 0.1980 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 1.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.087 15340 Z= 0.159 Angle : 0.572 13.438 20787 Z= 0.277 Chirality : 0.043 0.215 2431 Planarity : 0.003 0.025 2782 Dihedral : 5.630 62.545 2145 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.56 % 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: -1.03 (0.29), residues: 260 sheet: 1.06 (0.22), residues: 559 loop : -0.34 (0.16), residues: 1274 *********************** 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 165 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 158 average time/residue: 0.2296 time to fit residues: 57.8705 Evaluate side-chains 137 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 1.895 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1539 time to fit residues: 4.5852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 40.0000 chunk 192 optimal weight: 80.0000 chunk 175 optimal weight: 20.0000 chunk 186 optimal weight: 50.0000 chunk 112 optimal weight: 30.0000 chunk 81 optimal weight: 30.0000 chunk 146 optimal weight: 10.0000 chunk 57 optimal weight: 50.0000 chunk 168 optimal weight: 7.9990 chunk 176 optimal weight: 50.0000 chunk 122 optimal weight: 8.9990 overall best weight: 15.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 1.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 15340 Z= 0.350 Angle : 0.679 13.681 20787 Z= 0.338 Chirality : 0.044 0.199 2431 Planarity : 0.003 0.032 2782 Dihedral : 6.280 65.686 2145 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.07 (0.29), residues: 260 sheet: 1.14 (0.23), residues: 507 loop : -0.43 (0.16), residues: 1326 *********************** 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 141 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.820 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 137 average time/residue: 0.2249 time to fit residues: 50.2450 Evaluate side-chains 122 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.850 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1416 time to fit residues: 4.3248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 93 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 chunk 190 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 17 optimal weight: 30.0000 chunk 127 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN F 70 ASN G 37 GLN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 1.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 15340 Z= 0.215 Angle : 0.617 13.719 20787 Z= 0.300 Chirality : 0.044 0.192 2431 Planarity : 0.003 0.032 2782 Dihedral : 5.987 68.976 2145 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.37 % 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: -0.11 (0.17), residues: 2093 helix: -1.04 (0.29), residues: 260 sheet: 1.19 (0.23), residues: 507 loop : -0.35 (0.16), residues: 1326 ********************** 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 138 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 1.534 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 134 average time/residue: 0.2106 time to fit residues: 46.3056 Evaluate side-chains 125 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.682 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1524 time to fit residues: 3.5272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 40.0000 chunk 165 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 169 optimal weight: 40.0000 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 40.0000 chunk 145 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN ** H 163 GLN ** 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 = 0.3191 r_free = 0.3191 target = 0.060367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.051237 restraints weight = 71423.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.052677 restraints weight = 41570.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.053573 restraints weight = 27739.749| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 1.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 15340 Z= 0.183 Angle : 0.597 14.178 20787 Z= 0.287 Chirality : 0.044 0.173 2431 Planarity : 0.003 0.025 2782 Dihedral : 5.690 66.396 2145 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.01 (0.29), residues: 260 sheet: 1.05 (0.22), residues: 559 loop : -0.34 (0.16), residues: 1274 =============================================================================== Job complete usr+sys time: 2344.66 seconds wall clock time: 44 minutes 34.86 seconds (2674.86 seconds total)