Starting phenix.real_space_refine on Thu May 15 07:10:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pp6_17796/05_2025/8pp6_17796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pp6_17796/05_2025/8pp6_17796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pp6_17796/05_2025/8pp6_17796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pp6_17796/05_2025/8pp6_17796.map" model { file = "/net/cci-nas-00/data/ceres_data/8pp6_17796/05_2025/8pp6_17796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pp6_17796/05_2025/8pp6_17796.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 311 5.49 5 S 19 5.16 5 C 7396 2.51 5 N 2487 2.21 5 O 3104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13318 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 808 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 742 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 753 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3180 Classifications: {'DNA': 156} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 155} Chain: "J" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3214 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "K" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 283 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "M" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12495 SG CYS K 27 64.981 84.416 37.321 1.00133.28 S ATOM 12514 SG CYS K 30 63.315 85.615 34.414 1.00141.72 S ATOM 12602 SG CYS K 41 62.188 86.617 38.206 1.00135.85 S ATOM 12622 SG CYS K 44 61.221 83.403 36.536 1.00137.92 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LYS A 36 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 36 " occ=0.00 residue: pdb=" N ARG A 129 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG A 129 " occ=0.00 residue: pdb=" N LYS E 36 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS E 36 " occ=0.00 residue: pdb=" N LYS H 122 " occ=0.00 ... (8 atoms not shown) pdb=" OXT LYS H 122 " occ=0.00 Time building chain proxies: 7.31, per 1000 atoms: 0.55 Number of scatterers: 13318 At special positions: 0 Unit cell: (117.058, 124.716, 123.622, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 19 16.00 P 311 15.00 O 3104 8.00 N 2487 7.00 C 7396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 975.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 27 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 44 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 30 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 41 " Number of angles added : 6 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1634 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 66.2% alpha, 4.6% beta 139 base pairs and 284 stacking pairs defined. Time for finding SS restraints: 5.61 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.096A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.562A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.072A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.586A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 44 through 72 removed outlier: 4.547A pdb=" N VAL C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 89 removed outlier: 3.552A pdb=" N LEU C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.555A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.546A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.524A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.059A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 15 through 21 Processing helix chain 'G' and resid 25 through 35 Processing helix chain 'G' and resid 44 through 72 removed outlier: 4.346A pdb=" N VAL G 48 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL G 61 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 89 removed outlier: 3.743A pdb=" N LEU G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.866A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'M' and resid 22 through 34 removed outlier: 3.521A pdb=" N VAL M 26 " --> pdb=" O THR M 22 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE M 30 " --> pdb=" O VAL M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.867A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 removed outlier: 7.060A pdb=" N ARG C 41 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 99 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 41 through 42 removed outlier: 7.071A pdb=" N ARG G 41 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 76 through 77 Processing sheet with id=AA9, first strand: chain 'K' and resid 24 through 25 Processing sheet with id=AB1, first strand: chain 'M' and resid 12 through 16 removed outlier: 3.844A pdb=" N LEU M 69 " --> pdb=" O LYS M 6 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 720 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 284 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2782 1.33 - 1.46: 4521 1.46 - 1.58: 6230 1.58 - 1.70: 621 1.70 - 1.82: 32 Bond restraints: 14186 Sorted by residual: bond pdb=" CB THR F 71 " pdb=" CG2 THR F 71 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.37e+00 bond pdb=" C4' DC I 70 " pdb=" O4' DC I 70 " ideal model delta sigma weight residual 1.450 1.428 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C3' DT J 14 " pdb=" C2' DT J 14 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" O4' DC I 10 " pdb=" C1' DC I 10 " ideal model delta sigma weight residual 1.414 1.394 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" O4' DT J 9 " pdb=" C1' DT J 9 " ideal model delta sigma weight residual 1.414 1.395 0.019 2.00e-02 2.50e+03 9.30e-01 ... (remaining 14181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 19277 1.10 - 2.20: 973 2.20 - 3.29: 213 3.29 - 4.39: 13 4.39 - 5.49: 9 Bond angle restraints: 20485 Sorted by residual: angle pdb=" N THR K 31 " pdb=" CA THR K 31 " pdb=" CB THR K 31 " ideal model delta sigma weight residual 113.65 109.91 3.74 1.47e+00 4.63e-01 6.46e+00 angle pdb=" N THR K 31 " pdb=" CA THR K 31 " pdb=" C THR K 31 " ideal model delta sigma weight residual 113.72 110.04 3.68 1.52e+00 4.33e-01 5.85e+00 angle pdb=" C3' DC I 5 " pdb=" C2' DC I 5 " pdb=" C1' DC I 5 " ideal model delta sigma weight residual 101.60 98.07 3.53 1.50e+00 4.44e-01 5.55e+00 angle pdb=" CB LYS K 54 " pdb=" CG LYS K 54 " pdb=" CD LYS K 54 " ideal model delta sigma weight residual 111.30 116.27 -4.97 2.30e+00 1.89e-01 4.67e+00 angle pdb=" C VAL F 70 " pdb=" N THR F 71 " pdb=" CA THR F 71 " ideal model delta sigma weight residual 120.31 117.16 3.15 1.52e+00 4.33e-01 4.28e+00 ... (remaining 20480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.13: 5751 26.13 - 52.25: 1670 52.25 - 78.38: 336 78.38 - 104.50: 1 104.50 - 130.63: 1 Dihedral angle restraints: 7759 sinusoidal: 5232 harmonic: 2527 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 89.37 130.63 1 3.50e+01 8.16e-04 1.29e+01 dihedral pdb=" CG ARG C 70 " pdb=" CD ARG C 70 " pdb=" NE ARG C 70 " pdb=" CZ ARG C 70 " ideal model delta sinusoidal sigma weight residual 90.00 134.18 -44.18 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG F 78 " pdb=" CD ARG F 78 " pdb=" NE ARG F 78 " pdb=" CZ ARG F 78 " ideal model delta sinusoidal sigma weight residual -180.00 -136.22 -43.78 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 7756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1295 0.025 - 0.049: 711 0.049 - 0.074: 224 0.074 - 0.099: 56 0.099 - 0.123: 41 Chirality restraints: 2327 Sorted by residual: chirality pdb=" CA ILE G 78 " pdb=" N ILE G 78 " pdb=" C ILE G 78 " pdb=" CB ILE G 78 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA PRO D 47 " pdb=" N PRO D 47 " pdb=" C PRO D 47 " pdb=" CB PRO D 47 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 2324 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.025 2.00e-02 2.50e+03 1.05e-02 3.29e+00 pdb=" N9 DG I 47 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -55 " -0.021 2.00e-02 2.50e+03 9.12e-03 2.50e+00 pdb=" N9 DG I -55 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DG I -55 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I -55 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I -55 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I -55 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG I -55 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I -55 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I -55 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -55 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I -55 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG I -55 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 36 " 0.021 2.00e-02 2.50e+03 1.03e-02 2.41e+00 pdb=" N1 DC I 36 " -0.019 2.00e-02 2.50e+03 pdb=" C2 DC I 36 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 36 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DC I 36 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 36 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 36 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 36 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC I 36 " -0.005 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2422 2.79 - 3.32: 10621 3.32 - 3.85: 24345 3.85 - 4.37: 29835 4.37 - 4.90: 41911 Nonbonded interactions: 109134 Sorted by model distance: nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.263 3.040 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.360 3.040 nonbonded pdb=" OE1 GLU H 73 " pdb=" NH2 ARG H 76 " model vdw 2.398 3.120 nonbonded pdb=" O LEU E 61 " pdb=" NH1 ARG F 36 " model vdw 2.419 3.120 nonbonded pdb=" OG1 THR D 85 " pdb=" OP1 DA J -34 " model vdw 2.429 3.040 ... (remaining 109129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 36 through 133) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 29 through 122) } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 34.860 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.005 0.039 14190 Z= 0.204 Angle : 0.579 13.065 20491 Z= 0.338 Chirality : 0.035 0.123 2327 Planarity : 0.004 0.046 1513 Dihedral : 26.622 130.630 6125 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.14 % Allowed : 11.19 % Favored : 88.68 % 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: 1.64 (0.28), residues: 852 helix: 2.20 (0.22), residues: 542 sheet: 0.73 (1.53), residues: 18 loop : -1.10 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 25 HIS 0.003 0.001 HIS E 39 PHE 0.015 0.002 PHE K 39 TYR 0.012 0.002 TYR B 72 ARG 0.008 0.001 ARG G 70 Details of bonding type rmsd hydrogen bonds : bond 0.13402 ( 790) hydrogen bonds : angle 3.74001 ( 1971) metal coordination : bond 0.00683 ( 4) metal coordination : angle 7.86947 ( 6) covalent geometry : bond 0.00454 (14186) covalent geometry : angle 0.56294 (20485) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 LYS cc_start: 0.7642 (tttp) cc_final: 0.7429 (tttm) REVERT: K 25 TRP cc_start: 0.8057 (p-90) cc_final: 0.7686 (p-90) outliers start: 1 outliers final: 1 residues processed: 318 average time/residue: 0.3320 time to fit residues: 138.6439 Evaluate side-chains 256 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.0870 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 93 GLN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS G 83 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.081557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.053173 restraints weight = 36768.001| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.69 r_work: 0.2680 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14190 Z= 0.257 Angle : 0.638 16.057 20491 Z= 0.363 Chirality : 0.037 0.127 2327 Planarity : 0.005 0.031 1513 Dihedral : 29.518 132.997 4377 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.37 % Allowed : 17.05 % Favored : 78.58 % 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: 1.97 (0.29), residues: 852 helix: 2.49 (0.22), residues: 549 sheet: -0.66 (1.33), residues: 17 loop : -1.02 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP K 25 HIS 0.004 0.001 HIS B 75 PHE 0.013 0.002 PHE E 67 TYR 0.026 0.002 TYR H 80 ARG 0.009 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.06014 ( 790) hydrogen bonds : angle 3.18598 ( 1971) metal coordination : bond 0.01192 ( 4) metal coordination : angle 10.77156 ( 6) covalent geometry : bond 0.00582 (14186) covalent geometry : angle 0.61132 (20485) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 267 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8620 (mmp80) cc_final: 0.8037 (mmm-85) REVERT: B 88 TYR cc_start: 0.8915 (m-10) cc_final: 0.8673 (m-10) REVERT: D 32 GLU cc_start: 0.8442 (pt0) cc_final: 0.8169 (pt0) REVERT: E 120 MET cc_start: 0.8913 (mtm) cc_final: 0.8271 (mtm) REVERT: M 45 PHE cc_start: 0.8384 (t80) cc_final: 0.7884 (t80) outliers start: 32 outliers final: 20 residues processed: 278 average time/residue: 0.3063 time to fit residues: 114.2841 Evaluate side-chains 262 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 55 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.083263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.055217 restraints weight = 37140.745| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.64 r_work: 0.2734 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14190 Z= 0.169 Angle : 0.564 10.693 20491 Z= 0.329 Chirality : 0.033 0.151 2327 Planarity : 0.004 0.036 1513 Dihedral : 29.273 130.548 4375 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.14 % Allowed : 20.74 % Favored : 76.13 % 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: 2.23 (0.29), residues: 852 helix: 2.73 (0.22), residues: 548 sheet: -0.98 (1.02), residues: 28 loop : -0.93 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K 25 HIS 0.003 0.001 HIS F 75 PHE 0.016 0.002 PHE K 39 TYR 0.028 0.002 TYR H 80 ARG 0.009 0.001 ARG K 33 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 790) hydrogen bonds : angle 2.79659 ( 1971) metal coordination : bond 0.00961 ( 4) metal coordination : angle 6.44521 ( 6) covalent geometry : bond 0.00367 (14186) covalent geometry : angle 0.55325 (20485) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 256 time to evaluate : 1.035 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 63 ARG cc_start: 0.8504 (mmp80) cc_final: 0.7956 (mmm-85) REVERT: B 88 TYR cc_start: 0.8948 (m-10) cc_final: 0.8641 (m-10) REVERT: D 32 GLU cc_start: 0.8326 (pt0) cc_final: 0.7998 (pt0) REVERT: E 42 ARG cc_start: 0.8993 (mtp180) cc_final: 0.8657 (mtp85) REVERT: E 59 GLU cc_start: 0.8114 (pm20) cc_final: 0.7871 (pm20) REVERT: E 94 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8463 (tt0) REVERT: E 120 MET cc_start: 0.8863 (mtm) cc_final: 0.8268 (mtm) REVERT: F 25 ASN cc_start: 0.8952 (m-40) cc_final: 0.8618 (m-40) REVERT: K 47 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.7711 (mpp80) REVERT: M 44 ILE cc_start: 0.8798 (mm) cc_final: 0.8500 (tp) REVERT: M 45 PHE cc_start: 0.8428 (t80) cc_final: 0.8227 (t80) outliers start: 23 outliers final: 16 residues processed: 264 average time/residue: 0.3094 time to fit residues: 109.6585 Evaluate side-chains 262 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 246 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 0.0050 chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.082417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.054384 restraints weight = 37018.607| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.63 r_work: 0.2717 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14190 Z= 0.194 Angle : 0.566 11.212 20491 Z= 0.331 Chirality : 0.034 0.126 2327 Planarity : 0.004 0.037 1513 Dihedral : 29.247 131.024 4375 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.14 % Allowed : 21.96 % Favored : 74.90 % 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: 2.34 (0.29), residues: 852 helix: 2.81 (0.22), residues: 548 sheet: -0.91 (1.06), residues: 28 loop : -0.90 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 25 HIS 0.004 0.001 HIS F 75 PHE 0.015 0.002 PHE K 32 TYR 0.037 0.002 TYR H 80 ARG 0.008 0.001 ARG K 33 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 790) hydrogen bonds : angle 2.80761 ( 1971) metal coordination : bond 0.00818 ( 4) metal coordination : angle 4.64540 ( 6) covalent geometry : bond 0.00427 (14186) covalent geometry : angle 0.56045 (20485) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 249 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8967 (m-10) cc_final: 0.8656 (m-10) REVERT: C 34 ARG cc_start: 0.8771 (mtm110) cc_final: 0.8433 (ttm-80) REVERT: D 32 GLU cc_start: 0.8246 (pt0) cc_final: 0.7845 (pt0) REVERT: D 98 LEU cc_start: 0.8884 (mm) cc_final: 0.8600 (mm) REVERT: E 42 ARG cc_start: 0.9035 (mtp180) cc_final: 0.8695 (mtp85) REVERT: E 94 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8447 (tt0) REVERT: F 25 ASN cc_start: 0.8946 (m-40) cc_final: 0.8620 (m-40) REVERT: H 102 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8302 (mm-30) REVERT: K 47 ARG cc_start: 0.8241 (mtm-85) cc_final: 0.7528 (mpp80) REVERT: M 45 PHE cc_start: 0.8419 (t80) cc_final: 0.7647 (t80) outliers start: 23 outliers final: 17 residues processed: 257 average time/residue: 0.3047 time to fit residues: 105.8858 Evaluate side-chains 259 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 242 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.083203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.055181 restraints weight = 37433.784| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.64 r_work: 0.2739 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14190 Z= 0.172 Angle : 0.554 10.644 20491 Z= 0.325 Chirality : 0.033 0.125 2327 Planarity : 0.004 0.035 1513 Dihedral : 29.170 131.264 4375 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.55 % Allowed : 22.51 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.43 (0.29), residues: 852 helix: 2.89 (0.22), residues: 550 sheet: -0.89 (1.06), residues: 28 loop : -0.89 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 25 HIS 0.003 0.001 HIS F 75 PHE 0.015 0.001 PHE K 32 TYR 0.017 0.002 TYR C 56 ARG 0.006 0.000 ARG K 33 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 790) hydrogen bonds : angle 2.72161 ( 1971) metal coordination : bond 0.00657 ( 4) metal coordination : angle 3.88116 ( 6) covalent geometry : bond 0.00375 (14186) covalent geometry : angle 0.54985 (20485) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 THR cc_start: 0.8992 (m) cc_final: 0.8782 (t) REVERT: C 34 ARG cc_start: 0.8766 (mtm110) cc_final: 0.8429 (ttm-80) REVERT: D 80 TYR cc_start: 0.8202 (m-10) cc_final: 0.7986 (m-80) REVERT: D 117 LYS cc_start: 0.9236 (ttmm) cc_final: 0.8617 (ttpp) REVERT: E 42 ARG cc_start: 0.9017 (mtp180) cc_final: 0.8681 (mtp85) REVERT: F 25 ASN cc_start: 0.8948 (m-40) cc_final: 0.8645 (m-40) REVERT: G 32 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9064 (mm) REVERT: H 102 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8217 (mm-30) REVERT: K 47 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7430 (mpp80) REVERT: M 43 LEU cc_start: 0.9067 (mm) cc_final: 0.8618 (pt) REVERT: M 45 PHE cc_start: 0.8502 (t80) cc_final: 0.7663 (t80) outliers start: 26 outliers final: 18 residues processed: 259 average time/residue: 0.2956 time to fit residues: 103.5596 Evaluate side-chains 262 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 26 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 70 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.083780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.055898 restraints weight = 37588.798| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.67 r_work: 0.2753 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14190 Z= 0.163 Angle : 0.552 10.756 20491 Z= 0.323 Chirality : 0.032 0.125 2327 Planarity : 0.004 0.033 1513 Dihedral : 29.121 131.828 4375 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.00 % Allowed : 23.06 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.54 (0.29), residues: 852 helix: 2.98 (0.22), residues: 553 sheet: -0.91 (1.01), residues: 28 loop : -0.91 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 25 HIS 0.003 0.001 HIS F 75 PHE 0.015 0.001 PHE K 32 TYR 0.018 0.002 TYR C 56 ARG 0.008 0.000 ARG K 33 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 790) hydrogen bonds : angle 2.68290 ( 1971) metal coordination : bond 0.00524 ( 4) metal coordination : angle 3.26629 ( 6) covalent geometry : bond 0.00352 (14186) covalent geometry : angle 0.54923 (20485) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.9037 (ttp80) cc_final: 0.8827 (tmm-80) REVERT: C 34 ARG cc_start: 0.8766 (mtm110) cc_final: 0.8430 (ttm-80) REVERT: D 117 LYS cc_start: 0.9217 (ttmm) cc_final: 0.8607 (ttpp) REVERT: E 42 ARG cc_start: 0.9078 (mtp180) cc_final: 0.8743 (mtp85) REVERT: E 94 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8305 (tt0) REVERT: G 32 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9063 (mm) REVERT: K 47 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7459 (mpp80) REVERT: M 43 LEU cc_start: 0.9042 (mm) cc_final: 0.8614 (pt) REVERT: M 45 PHE cc_start: 0.8494 (t80) cc_final: 0.7627 (t80) outliers start: 22 outliers final: 16 residues processed: 254 average time/residue: 0.3000 time to fit residues: 102.8070 Evaluate side-chains 261 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 11 optimal weight: 0.0670 overall best weight: 2.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.082880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.055118 restraints weight = 37237.579| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.63 r_work: 0.2727 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14190 Z= 0.197 Angle : 0.575 12.088 20491 Z= 0.334 Chirality : 0.034 0.128 2327 Planarity : 0.004 0.034 1513 Dihedral : 29.171 132.301 4375 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.09 % Allowed : 22.65 % Favored : 73.26 % 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: 2.42 (0.29), residues: 852 helix: 2.86 (0.22), residues: 553 sheet: -1.16 (0.98), residues: 28 loop : -0.87 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP K 25 HIS 0.003 0.001 HIS F 75 PHE 0.016 0.001 PHE K 32 TYR 0.024 0.002 TYR D 80 ARG 0.008 0.000 ARG K 33 Details of bonding type rmsd hydrogen bonds : bond 0.04643 ( 790) hydrogen bonds : angle 2.81226 ( 1971) metal coordination : bond 0.00627 ( 4) metal coordination : angle 3.30078 ( 6) covalent geometry : bond 0.00438 (14186) covalent geometry : angle 0.57262 (20485) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.9043 (ttp80) cc_final: 0.8816 (tmm-80) REVERT: C 34 ARG cc_start: 0.8756 (mtm110) cc_final: 0.8418 (ttm-80) REVERT: E 42 ARG cc_start: 0.9087 (mtp180) cc_final: 0.8657 (mtp85) REVERT: F 25 ASN cc_start: 0.9087 (m-40) cc_final: 0.8551 (m-40) REVERT: G 32 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9069 (mm) REVERT: H 76 ARG cc_start: 0.9034 (ttm-80) cc_final: 0.8703 (ttp80) REVERT: K 47 ARG cc_start: 0.8215 (mtm-85) cc_final: 0.7501 (mpp80) REVERT: K 48 LYS cc_start: 0.8554 (tttp) cc_final: 0.8214 (tttm) REVERT: M 43 LEU cc_start: 0.9040 (mm) cc_final: 0.8526 (pt) REVERT: M 45 PHE cc_start: 0.8491 (t80) cc_final: 0.7637 (t80) outliers start: 30 outliers final: 23 residues processed: 259 average time/residue: 0.2992 time to fit residues: 104.3762 Evaluate side-chains 262 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.082518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.054710 restraints weight = 37526.114| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.65 r_work: 0.2716 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14190 Z= 0.209 Angle : 0.592 12.070 20491 Z= 0.343 Chirality : 0.034 0.133 2327 Planarity : 0.004 0.035 1513 Dihedral : 29.203 132.416 4375 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.68 % Allowed : 23.87 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.29), residues: 852 helix: 2.76 (0.22), residues: 553 sheet: -1.33 (0.95), residues: 28 loop : -0.84 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 25 HIS 0.003 0.001 HIS E 113 PHE 0.018 0.002 PHE K 32 TYR 0.038 0.002 TYR B 88 ARG 0.010 0.000 ARG K 33 Details of bonding type rmsd hydrogen bonds : bond 0.04816 ( 790) hydrogen bonds : angle 2.90326 ( 1971) metal coordination : bond 0.00694 ( 4) metal coordination : angle 3.12710 ( 6) covalent geometry : bond 0.00467 (14186) covalent geometry : angle 0.58957 (20485) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.9054 (ttp80) cc_final: 0.8824 (tmm-80) REVERT: C 34 ARG cc_start: 0.8749 (mtm110) cc_final: 0.8408 (ttm-80) REVERT: E 42 ARG cc_start: 0.9132 (mtp180) cc_final: 0.8706 (mtp85) REVERT: G 32 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9073 (mm) REVERT: K 47 ARG cc_start: 0.8251 (mtm-85) cc_final: 0.7559 (mpp80) REVERT: M 43 LEU cc_start: 0.9040 (mm) cc_final: 0.8484 (pt) REVERT: M 45 PHE cc_start: 0.8479 (t80) cc_final: 0.7625 (t80) outliers start: 27 outliers final: 23 residues processed: 257 average time/residue: 0.3117 time to fit residues: 107.8514 Evaluate side-chains 261 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 3.9990 chunk 53 optimal weight: 0.0040 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 106 optimal weight: 40.0000 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN M 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.084028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.056532 restraints weight = 37104.812| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.72 r_work: 0.2759 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14190 Z= 0.162 Angle : 0.580 12.587 20491 Z= 0.336 Chirality : 0.033 0.127 2327 Planarity : 0.004 0.034 1513 Dihedral : 29.088 131.890 4375 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.14 % Allowed : 24.56 % Favored : 72.31 % 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: 2.43 (0.29), residues: 852 helix: 2.85 (0.22), residues: 553 sheet: -1.32 (0.94), residues: 28 loop : -0.79 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 25 HIS 0.003 0.001 HIS E 113 PHE 0.015 0.001 PHE K 32 TYR 0.031 0.002 TYR D 80 ARG 0.005 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 790) hydrogen bonds : angle 2.76848 ( 1971) metal coordination : bond 0.00466 ( 4) metal coordination : angle 2.42178 ( 6) covalent geometry : bond 0.00351 (14186) covalent geometry : angle 0.57852 (20485) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.9031 (m-40) cc_final: 0.8606 (m-40) REVERT: B 79 LYS cc_start: 0.9390 (mtpp) cc_final: 0.8968 (ttmm) REVERT: C 34 ARG cc_start: 0.8709 (mtm110) cc_final: 0.8392 (ttm-80) REVERT: D 80 TYR cc_start: 0.8020 (m-10) cc_final: 0.7747 (m-80) REVERT: E 42 ARG cc_start: 0.9080 (mtp180) cc_final: 0.8663 (mtp85) REVERT: G 32 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9070 (mm) REVERT: H 76 ARG cc_start: 0.9053 (ttm-80) cc_final: 0.8665 (ttp80) REVERT: K 47 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7511 (mpp80) REVERT: M 43 LEU cc_start: 0.9000 (mm) cc_final: 0.8469 (pt) REVERT: M 45 PHE cc_start: 0.8485 (t80) cc_final: 0.7640 (t80) outliers start: 23 outliers final: 19 residues processed: 262 average time/residue: 0.3011 time to fit residues: 106.1906 Evaluate side-chains 260 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 37 ASN M 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.083479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.055979 restraints weight = 37478.665| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.69 r_work: 0.2757 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14190 Z= 0.178 Angle : 0.588 12.160 20491 Z= 0.340 Chirality : 0.033 0.162 2327 Planarity : 0.004 0.035 1513 Dihedral : 29.112 131.937 4375 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.27 % Allowed : 24.97 % Favored : 71.76 % 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: 2.31 (0.29), residues: 852 helix: 2.74 (0.22), residues: 559 sheet: -1.15 (0.91), residues: 28 loop : -0.91 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 25 HIS 0.004 0.001 HIS E 113 PHE 0.012 0.001 PHE E 67 TYR 0.032 0.002 TYR B 88 ARG 0.005 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 790) hydrogen bonds : angle 2.80818 ( 1971) metal coordination : bond 0.00540 ( 4) metal coordination : angle 2.49783 ( 6) covalent geometry : bond 0.00391 (14186) covalent geometry : angle 0.58603 (20485) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9395 (mtpp) cc_final: 0.8978 (ttmm) REVERT: B 92 ARG cc_start: 0.8779 (tmm-80) cc_final: 0.8440 (tpt-90) REVERT: C 34 ARG cc_start: 0.8729 (mtm110) cc_final: 0.8399 (ttm-80) REVERT: D 117 LYS cc_start: 0.9231 (ttmm) cc_final: 0.8735 (ttpt) REVERT: E 42 ARG cc_start: 0.9053 (mtp180) cc_final: 0.8639 (mtp85) REVERT: F 25 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8659 (m-40) REVERT: G 32 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9092 (mm) REVERT: H 76 ARG cc_start: 0.9137 (ttm-80) cc_final: 0.8831 (ttp80) REVERT: K 33 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7821 (mmm-85) REVERT: K 47 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.7545 (mpp80) REVERT: K 48 LYS cc_start: 0.8563 (tttp) cc_final: 0.8230 (tttm) REVERT: M 43 LEU cc_start: 0.9012 (mm) cc_final: 0.8463 (pt) REVERT: M 45 PHE cc_start: 0.8461 (t80) cc_final: 0.7611 (t80) outliers start: 24 outliers final: 19 residues processed: 255 average time/residue: 0.3238 time to fit residues: 113.1330 Evaluate side-chains 260 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 0.0020 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN M 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.085484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.058210 restraints weight = 37243.518| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.70 r_work: 0.2810 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14190 Z= 0.150 Angle : 0.577 12.989 20491 Z= 0.334 Chirality : 0.032 0.145 2327 Planarity : 0.004 0.033 1513 Dihedral : 29.006 131.192 4375 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.05 % Allowed : 26.33 % Favored : 71.62 % 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: 2.37 (0.29), residues: 852 helix: 2.78 (0.22), residues: 557 sheet: -0.85 (0.93), residues: 28 loop : -0.88 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 25 HIS 0.004 0.001 HIS E 113 PHE 0.013 0.001 PHE K 32 TYR 0.040 0.002 TYR B 88 ARG 0.006 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 790) hydrogen bonds : angle 2.66206 ( 1971) metal coordination : bond 0.00412 ( 4) metal coordination : angle 2.05901 ( 6) covalent geometry : bond 0.00317 (14186) covalent geometry : angle 0.57627 (20485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7906.18 seconds wall clock time: 136 minutes 18.09 seconds (8178.09 seconds total)