Starting phenix.real_space_refine on Sat Mar 16 10:02:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f86_28915/03_2024/8f86_28915_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f86_28915/03_2024/8f86_28915.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f86_28915/03_2024/8f86_28915_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f86_28915/03_2024/8f86_28915_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f86_28915/03_2024/8f86_28915_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f86_28915/03_2024/8f86_28915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f86_28915/03_2024/8f86_28915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f86_28915/03_2024/8f86_28915_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f86_28915/03_2024/8f86_28915_updated.pdb" } resolution = 3.1 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= 0.011 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 297 5.49 5 S 22 5.16 5 C 8111 2.51 5 N 2698 2.21 5 O 3271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 133": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14400 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 868 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 861 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 106} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3050 Classifications: {'DNA': 148} Link IDs: {'rna3p': 147} Chain: "J" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3015 Classifications: {'DNA': 148} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 147} Chain: "K" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2242 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 270} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'ZSL': 1} Classifications: {'undetermined': 1} 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 13207 SG CYS K 141 67.069 70.011 64.643 1.00144.83 S ATOM 13227 SG CYS K 144 69.022 69.847 67.742 1.00126.49 S ATOM 13392 SG CYS K 166 69.504 67.199 65.177 1.00126.37 S ATOM 13470 SG CYS K 177 66.155 67.223 67.101 1.00122.41 S Time building chain proxies: 8.56, per 1000 atoms: 0.59 Number of scatterers: 14400 At special positions: 0 Unit cell: (116.2, 134.46, 119.52, 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 22 16.00 P 297 15.00 O 3271 8.00 N 2698 7.00 C 8111 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM14390 O37 ZSL A 201 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.87 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 141 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 166 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 144 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 177 " Number of angles added : 6 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 2 sheets defined 53.6% alpha, 2.0% beta 147 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 7.74 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.912A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 48 through 75 removed outlier: 3.597A pdb=" N TYR B 51 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 52 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 47 through 73 Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.780A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.554A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.866A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 73 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 119 Processing helix chain 'K' and resid 27 through 43 removed outlier: 4.015A pdb=" N GLN K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 59 removed outlier: 3.896A pdb=" N SER K 59 " --> pdb=" O ILE K 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 55 through 59' Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 93 through 104 Processing helix chain 'K' and resid 118 through 121 No H-bonds generated for 'chain 'K' and resid 118 through 121' Processing helix chain 'K' and resid 194 through 206 Processing helix chain 'K' and resid 221 through 223 No H-bonds generated for 'chain 'K' and resid 221 through 223' Processing helix chain 'K' and resid 225 through 230 removed outlier: 3.841A pdb=" N LYS K 230 " --> pdb=" O PRO K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 269 Processing sheet with id= A, first strand: chain 'K' and resid 252 through 254 removed outlier: 3.574A pdb=" N ILE K 254 " --> pdb=" O ILE K 238 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL K 48 " --> pdb=" O LEU K 209 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N PHE K 49 " --> pdb=" O ARG K 108 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU K 110 " --> pdb=" O PHE K 49 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR K 51 " --> pdb=" O LEU K 110 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 138 through 140 396 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 379 hydrogen bonds 758 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 5.92 Time building geometry restraints manager: 8.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3963 1.34 - 1.47: 4876 1.47 - 1.60: 5835 1.60 - 1.72: 551 1.72 - 1.85: 39 Bond restraints: 15264 Sorted by residual: bond pdb=" C20 ZSL A 201 " pdb=" S46 ZSL A 201 " ideal model delta sigma weight residual 1.388 1.746 -0.358 2.00e-02 2.50e+03 3.21e+02 bond pdb=" C19 ZSL A 201 " pdb=" O34 ZSL A 201 " ideal model delta sigma weight residual 1.592 1.342 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C21 ZSL A 201 " pdb=" C23 ZSL A 201 " ideal model delta sigma weight residual 1.284 1.518 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C24 ZSL A 201 " pdb=" C26 ZSL A 201 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.27e+01 bond pdb=" C18 ZSL A 201 " pdb=" O33 ZSL A 201 " ideal model delta sigma weight residual 1.597 1.411 0.186 2.00e-02 2.50e+03 8.61e+01 ... (remaining 15259 not shown) Histogram of bond angle deviations from ideal: 80.66 - 91.78: 2 91.78 - 102.91: 303 102.91 - 114.04: 10376 114.04 - 125.17: 10172 125.17 - 136.29: 1050 Bond angle restraints: 21903 Sorted by residual: angle pdb=" O3' DG I 20 " pdb=" P DG I 21 " pdb=" OP1 DG I 21 " ideal model delta sigma weight residual 108.00 80.66 27.34 3.00e+00 1.11e-01 8.31e+01 angle pdb=" O3' DG I 20 " pdb=" P DG I 21 " pdb=" OP2 DG I 21 " ideal model delta sigma weight residual 108.00 87.49 20.51 3.00e+00 1.11e-01 4.67e+01 angle pdb=" N03 ZSL A 201 " pdb=" C28 ZSL A 201 " pdb=" N05 ZSL A 201 " ideal model delta sigma weight residual 103.55 122.63 -19.08 3.00e+00 1.11e-01 4.04e+01 angle pdb=" C27 ZSL A 201 " pdb=" C28 ZSL A 201 " pdb=" N05 ZSL A 201 " ideal model delta sigma weight residual 134.75 120.16 14.59 3.00e+00 1.11e-01 2.36e+01 angle pdb=" CA PRO K 221 " pdb=" N PRO K 221 " pdb=" CD PRO K 221 " ideal model delta sigma weight residual 112.00 105.90 6.10 1.40e+00 5.10e-01 1.90e+01 ... (remaining 21898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 7038 34.47 - 68.95: 1357 68.95 - 103.42: 23 103.42 - 137.89: 1 137.89 - 172.37: 2 Dihedral angle restraints: 8421 sinusoidal: 5383 harmonic: 3038 Sorted by residual: dihedral pdb=" C4' DC J 4 " pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " pdb=" P DC J 5 " ideal model delta sinusoidal sigma weight residual 220.00 47.63 172.37 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DT I -16 " ideal model delta sinusoidal sigma weight residual 220.00 59.57 160.43 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" C17 ZSL A 201 " pdb=" C18 ZSL A 201 " pdb=" N07 ZSL A 201 " pdb=" C29 ZSL A 201 " ideal model delta sinusoidal sigma weight residual -88.51 24.29 -112.80 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 8418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.406: 2494 0.406 - 0.813: 0 0.813 - 1.219: 0 1.219 - 1.626: 0 1.626 - 2.032: 1 Chirality restraints: 2495 Sorted by residual: chirality pdb=" P DG I 21 " pdb=" OP1 DG I 21 " pdb=" OP2 DG I 21 " pdb=" O5' DG I 21 " both_signs ideal model delta sigma weight residual True 2.35 0.31 2.03 2.00e-01 2.50e+01 1.03e+02 chirality pdb=" C20 ZSL A 201 " pdb=" C21 ZSL A 201 " pdb=" O36 ZSL A 201 " pdb=" S46 ZSL A 201 " both_signs ideal model delta sigma weight residual False 2.70 2.99 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C17 ZSL A 201 " pdb=" C16 ZSL A 201 " pdb=" C18 ZSL A 201 " pdb=" O32 ZSL A 201 " both_signs ideal model delta sigma weight residual False 2.41 2.69 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2492 not shown) Planarity restraints: 1751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 220 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO K 221 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO K 221 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO K 221 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC J -50 " -0.004 2.00e-02 2.50e+03 1.91e-02 8.20e+00 pdb=" N1 DC J -50 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DC J -50 " 0.047 2.00e-02 2.50e+03 pdb=" O2 DC J -50 " -0.030 2.00e-02 2.50e+03 pdb=" N3 DC J -50 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC J -50 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DC J -50 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC J -50 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC J -50 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 51 " -0.011 2.00e-02 2.50e+03 1.14e-02 3.91e+00 pdb=" N9 DG I 51 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DG I 51 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 51 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 51 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 51 " -0.015 2.00e-02 2.50e+03 pdb=" O6 DG I 51 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 51 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 51 " -0.024 2.00e-02 2.50e+03 pdb=" N2 DG I 51 " 0.015 2.00e-02 2.50e+03 pdb=" N3 DG I 51 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 51 " 0.004 2.00e-02 2.50e+03 ... (remaining 1748 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 87 2.52 - 3.12: 10666 3.12 - 3.71: 26040 3.71 - 4.31: 34981 4.31 - 4.90: 52019 Nonbonded interactions: 123793 Sorted by model distance: nonbonded pdb=" OG SER K 112 " pdb=" OD1 ASN K 114 " model vdw 1.927 2.440 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 1.966 2.440 nonbonded pdb=" OG1 THR K 244 " pdb=" OD1 ASP K 247 " model vdw 1.980 2.440 nonbonded pdb=" OD2 ASP K 63 " pdb=" O32 ZSL A 201 " model vdw 2.022 2.440 nonbonded pdb=" O LYS C 119 " pdb=" OG1 THR C 120 " model vdw 2.070 2.440 ... (remaining 123788 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' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 9.400 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 52.160 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.007 0.358 15264 Z= 0.439 Angle : 0.689 27.343 21903 Z= 0.379 Chirality : 0.057 2.032 2495 Planarity : 0.005 0.110 1751 Dihedral : 26.360 172.368 6461 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.22 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 21.33 % Favored : 78.67 % 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: 0.66 (0.27), residues: 1035 helix: 2.14 (0.21), residues: 610 sheet: -2.76 (0.79), residues: 44 loop : -2.14 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 276 HIS 0.004 0.001 HIS A 113 PHE 0.010 0.001 PHE A 67 TYR 0.014 0.001 TYR B 51 ARG 0.008 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8097 (mmm) cc_final: 0.7881 (mmm) REVERT: C 92 GLU cc_start: 0.8514 (mp0) cc_final: 0.8227 (mp0) REVERT: D 118 TYR cc_start: 0.8688 (t80) cc_final: 0.8391 (t80) REVERT: F 31 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8472 (mtpp) REVERT: F 77 LYS cc_start: 0.8789 (mttp) cc_final: 0.8521 (mmtt) REVERT: G 36 LYS cc_start: 0.8428 (tptp) cc_final: 0.8054 (tppt) REVERT: G 41 GLU cc_start: 0.8370 (tt0) cc_final: 0.8156 (mp0) REVERT: G 91 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7917 (tm-30) REVERT: H 32 GLU cc_start: 0.8066 (pt0) cc_final: 0.7854 (mt-10) REVERT: H 110 GLU cc_start: 0.7787 (tt0) cc_final: 0.7577 (mm-30) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.3384 time to fit residues: 52.7754 Evaluate side-chains 94 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 15264 Z= 0.306 Angle : 0.650 27.217 21903 Z= 0.363 Chirality : 0.056 2.038 2495 Planarity : 0.005 0.113 1751 Dihedral : 29.032 174.833 4416 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.54 % Favored : 95.27 % Rotamer: Outliers : 2.29 % Allowed : 20.53 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.27), residues: 1035 helix: 1.97 (0.21), residues: 605 sheet: -2.17 (1.06), residues: 24 loop : -1.73 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 71 HIS 0.005 0.001 HIS A 113 PHE 0.015 0.002 PHE A 67 TYR 0.027 0.002 TYR E 54 ARG 0.012 0.001 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8143 (mmm) cc_final: 0.7905 (mmm) REVERT: C 59 THR cc_start: 0.7738 (OUTLIER) cc_final: 0.7509 (t) REVERT: C 92 GLU cc_start: 0.8586 (mp0) cc_final: 0.7739 (mp0) REVERT: C 110 ASN cc_start: 0.7235 (p0) cc_final: 0.7002 (p0) REVERT: D 118 TYR cc_start: 0.8717 (t80) cc_final: 0.8433 (t80) REVERT: F 31 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8463 (mtpp) REVERT: F 77 LYS cc_start: 0.8798 (mttp) cc_final: 0.8531 (mmtt) REVERT: G 36 LYS cc_start: 0.8488 (tptp) cc_final: 0.8099 (tppt) REVERT: H 110 GLU cc_start: 0.7817 (tt0) cc_final: 0.7594 (mm-30) REVERT: K 5 TYR cc_start: 0.5185 (m-80) cc_final: 0.4580 (m-80) REVERT: K 35 TRP cc_start: 0.6935 (OUTLIER) cc_final: 0.6394 (m-90) REVERT: K 93 GLN cc_start: 0.8156 (tp40) cc_final: 0.7844 (tp-100) REVERT: K 136 MET cc_start: 0.7788 (mmm) cc_final: 0.7488 (mmm) REVERT: K 240 ASN cc_start: 0.8003 (t0) cc_final: 0.7791 (t0) REVERT: K 262 MET cc_start: 0.9038 (mtp) cc_final: 0.8715 (mtp) outliers start: 20 outliers final: 7 residues processed: 121 average time/residue: 0.3047 time to fit residues: 51.8374 Evaluate side-chains 104 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 212 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.0070 chunk 36 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN E 125 GLN H 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 15264 Z= 0.192 Angle : 0.604 26.937 21903 Z= 0.335 Chirality : 0.053 2.025 2495 Planarity : 0.005 0.109 1751 Dihedral : 28.883 174.215 4416 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.67 % Favored : 96.14 % Rotamer: Outliers : 2.41 % Allowed : 20.30 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1035 helix: 2.28 (0.21), residues: 598 sheet: -2.42 (0.96), residues: 24 loop : -1.49 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 71 HIS 0.005 0.001 HIS A 113 PHE 0.018 0.002 PHE K 49 TYR 0.012 0.001 TYR C 57 ARG 0.004 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.602 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.7945 (tp30) cc_final: 0.7307 (tt0) REVERT: B 84 MET cc_start: 0.8123 (mmm) cc_final: 0.7906 (mmm) REVERT: C 59 THR cc_start: 0.7649 (OUTLIER) cc_final: 0.7071 (m) REVERT: C 91 GLU cc_start: 0.7821 (tp30) cc_final: 0.7605 (tp30) REVERT: C 92 GLU cc_start: 0.8603 (mp0) cc_final: 0.7719 (mp0) REVERT: D 56 MET cc_start: 0.8509 (tpp) cc_final: 0.8238 (tpp) REVERT: D 118 TYR cc_start: 0.8675 (t80) cc_final: 0.8379 (t80) REVERT: E 125 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7088 (mp-120) REVERT: F 77 LYS cc_start: 0.8828 (mttp) cc_final: 0.8529 (mmtt) REVERT: G 36 LYS cc_start: 0.8493 (tptp) cc_final: 0.8161 (tptp) REVERT: H 110 GLU cc_start: 0.7791 (tt0) cc_final: 0.7579 (mm-30) REVERT: K 93 GLN cc_start: 0.8200 (tp40) cc_final: 0.7922 (tp-100) REVERT: K 240 ASN cc_start: 0.8033 (t0) cc_final: 0.7688 (t0) REVERT: K 262 MET cc_start: 0.8985 (mtp) cc_final: 0.8704 (mtp) outliers start: 21 outliers final: 12 residues processed: 118 average time/residue: 0.3038 time to fit residues: 50.9845 Evaluate side-chains 108 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 184 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 213 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 15264 Z= 0.411 Angle : 0.686 27.141 21903 Z= 0.381 Chirality : 0.058 2.011 2495 Planarity : 0.006 0.112 1751 Dihedral : 29.364 175.525 4416 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.41 % Favored : 94.40 % Rotamer: Outliers : 3.10 % Allowed : 21.10 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.27), residues: 1035 helix: 1.68 (0.21), residues: 602 sheet: -3.13 (0.64), residues: 40 loop : -1.63 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 71 HIS 0.006 0.001 HIS A 113 PHE 0.014 0.002 PHE A 67 TYR 0.018 0.002 TYR E 54 ARG 0.005 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8130 (tp30) cc_final: 0.7692 (tp30) REVERT: C 59 THR cc_start: 0.7753 (OUTLIER) cc_final: 0.7481 (t) REVERT: C 91 GLU cc_start: 0.7891 (tp30) cc_final: 0.7570 (tp30) REVERT: C 92 GLU cc_start: 0.8649 (mp0) cc_final: 0.8336 (mp0) REVERT: D 118 TYR cc_start: 0.8743 (t80) cc_final: 0.8515 (t80) REVERT: E 125 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: F 31 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8501 (mtpp) REVERT: F 77 LYS cc_start: 0.8796 (mttp) cc_final: 0.8531 (mmtt) REVERT: G 36 LYS cc_start: 0.8525 (tptp) cc_final: 0.8116 (tppt) REVERT: G 91 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7810 (tm-30) REVERT: G 95 LYS cc_start: 0.9068 (ttmm) cc_final: 0.8643 (mtmt) REVERT: H 110 GLU cc_start: 0.7833 (tt0) cc_final: 0.7614 (mm-30) REVERT: K 93 GLN cc_start: 0.8139 (tp40) cc_final: 0.7896 (tp-100) outliers start: 27 outliers final: 16 residues processed: 120 average time/residue: 0.3169 time to fit residues: 52.8222 Evaluate side-chains 114 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 184 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 125 GLN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 15264 Z= 0.232 Angle : 0.616 26.894 21903 Z= 0.342 Chirality : 0.054 2.015 2495 Planarity : 0.005 0.109 1751 Dihedral : 29.189 174.680 4416 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.57 % Favored : 96.23 % Rotamer: Outliers : 2.41 % Allowed : 22.36 % Favored : 75.23 % 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: 0.80 (0.27), residues: 1035 helix: 2.07 (0.21), residues: 600 sheet: -3.07 (0.69), residues: 34 loop : -1.61 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 71 HIS 0.006 0.001 HIS A 113 PHE 0.019 0.002 PHE K 49 TYR 0.011 0.001 TYR G 57 ARG 0.003 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8018 (tp30) cc_final: 0.7681 (tp30) REVERT: C 59 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7100 (m) REVERT: C 91 GLU cc_start: 0.7818 (tp30) cc_final: 0.7413 (tp30) REVERT: C 92 GLU cc_start: 0.8636 (mp0) cc_final: 0.8297 (mp0) REVERT: D 118 TYR cc_start: 0.8710 (t80) cc_final: 0.8413 (t80) REVERT: E 90 MET cc_start: 0.8122 (mmm) cc_final: 0.7869 (mmm) REVERT: E 125 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7328 (mp10) REVERT: F 77 LYS cc_start: 0.8806 (mttp) cc_final: 0.8537 (mmtt) REVERT: G 36 LYS cc_start: 0.8499 (tptp) cc_final: 0.8087 (tppt) REVERT: G 39 TYR cc_start: 0.8339 (m-80) cc_final: 0.8093 (m-80) REVERT: H 110 GLU cc_start: 0.7822 (tt0) cc_final: 0.7613 (mm-30) REVERT: K 5 TYR cc_start: 0.5303 (m-80) cc_final: 0.5087 (m-10) REVERT: K 93 GLN cc_start: 0.8167 (tp40) cc_final: 0.7863 (tp-100) REVERT: K 262 MET cc_start: 0.8954 (mtp) cc_final: 0.8698 (mtp) outliers start: 21 outliers final: 15 residues processed: 115 average time/residue: 0.3265 time to fit residues: 52.4172 Evaluate side-chains 112 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 177 CYS Chi-restraints excluded: chain K residue 184 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 120 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: A 68 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 15264 Z= 0.523 Angle : 0.758 27.555 21903 Z= 0.422 Chirality : 0.061 1.966 2495 Planarity : 0.006 0.112 1751 Dihedral : 29.812 175.934 4416 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.18 % Favored : 93.62 % Rotamer: Outliers : 3.90 % Allowed : 23.39 % Favored : 72.71 % 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: -0.14 (0.26), residues: 1035 helix: 1.19 (0.21), residues: 602 sheet: -3.33 (0.65), residues: 40 loop : -1.80 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 71 HIS 0.007 0.002 HIS A 113 PHE 0.017 0.003 PHE K 64 TYR 0.018 0.002 TYR E 54 ARG 0.006 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 94 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 59 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7565 (t) REVERT: C 91 GLU cc_start: 0.7962 (tp30) cc_final: 0.7497 (tp30) REVERT: C 92 GLU cc_start: 0.8691 (mp0) cc_final: 0.8377 (mp0) REVERT: D 118 TYR cc_start: 0.8768 (t80) cc_final: 0.8558 (t80) REVERT: E 125 GLN cc_start: 0.8145 (mp10) cc_final: 0.7834 (mp10) REVERT: F 77 LYS cc_start: 0.8782 (mttp) cc_final: 0.8524 (mmtt) REVERT: G 36 LYS cc_start: 0.8533 (tptp) cc_final: 0.8162 (tppt) REVERT: H 98 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7643 (mm) REVERT: H 110 GLU cc_start: 0.7846 (tt0) cc_final: 0.7627 (mm-30) outliers start: 34 outliers final: 19 residues processed: 125 average time/residue: 0.3008 time to fit residues: 53.5484 Evaluate side-chains 112 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 177 CYS Chi-restraints excluded: chain K residue 184 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN E 125 GLN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 15264 Z= 0.265 Angle : 0.644 26.917 21903 Z= 0.357 Chirality : 0.055 2.016 2495 Planarity : 0.005 0.109 1751 Dihedral : 29.517 174.601 4416 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.15 % Favored : 95.65 % Rotamer: Outliers : 2.98 % Allowed : 24.43 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1035 helix: 1.70 (0.21), residues: 602 sheet: -3.33 (0.69), residues: 34 loop : -1.59 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 71 HIS 0.006 0.001 HIS A 113 PHE 0.030 0.002 PHE K 49 TYR 0.015 0.002 TYR K 5 ARG 0.006 0.000 ARG K 172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 59 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7461 (t) REVERT: C 91 GLU cc_start: 0.7891 (tp30) cc_final: 0.7355 (tp30) REVERT: C 92 GLU cc_start: 0.8613 (mp0) cc_final: 0.8271 (mp0) REVERT: D 118 TYR cc_start: 0.8716 (t80) cc_final: 0.8491 (t80) REVERT: E 125 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: F 77 LYS cc_start: 0.8807 (mttp) cc_final: 0.8543 (mmtt) REVERT: G 36 LYS cc_start: 0.8542 (tptp) cc_final: 0.8155 (tppt) REVERT: H 98 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7691 (mm) REVERT: H 110 GLU cc_start: 0.7859 (tt0) cc_final: 0.7591 (tm-30) REVERT: K 5 TYR cc_start: 0.4711 (m-10) cc_final: 0.4272 (m-80) REVERT: K 49 PHE cc_start: 0.8352 (m-80) cc_final: 0.8045 (m-80) REVERT: K 93 GLN cc_start: 0.8224 (tp40) cc_final: 0.7964 (tp-100) REVERT: K 213 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6091 (mt) REVERT: K 262 MET cc_start: 0.8871 (mtp) cc_final: 0.8671 (mpp) outliers start: 26 outliers final: 20 residues processed: 116 average time/residue: 0.3152 time to fit residues: 51.9298 Evaluate side-chains 114 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 177 CYS Chi-restraints excluded: chain K residue 184 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 232 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 15264 Z= 0.387 Angle : 0.684 27.055 21903 Z= 0.380 Chirality : 0.057 1.996 2495 Planarity : 0.006 0.109 1751 Dihedral : 29.615 174.956 4416 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.70 % Favored : 94.11 % Rotamer: Outliers : 3.10 % Allowed : 24.08 % Favored : 72.82 % 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 (0.26), residues: 1035 helix: 1.53 (0.21), residues: 598 sheet: -3.36 (0.63), residues: 40 loop : -1.66 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 71 HIS 0.007 0.001 HIS A 113 PHE 0.047 0.003 PHE K 64 TYR 0.015 0.002 TYR G 50 ARG 0.006 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8347 (mm) REVERT: C 59 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7529 (t) REVERT: C 91 GLU cc_start: 0.7944 (tp30) cc_final: 0.7413 (tp30) REVERT: C 92 GLU cc_start: 0.8639 (mp0) cc_final: 0.8326 (mp0) REVERT: D 118 TYR cc_start: 0.8724 (t80) cc_final: 0.8492 (t80) REVERT: F 77 LYS cc_start: 0.8803 (mttp) cc_final: 0.8527 (mmtt) REVERT: G 36 LYS cc_start: 0.8503 (tptp) cc_final: 0.8123 (tppt) REVERT: G 91 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7825 (tm-30) REVERT: H 98 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7647 (mm) REVERT: H 110 GLU cc_start: 0.7870 (tt0) cc_final: 0.7563 (tm-30) REVERT: K 5 TYR cc_start: 0.4941 (m-10) cc_final: 0.4462 (m-80) REVERT: K 71 TRP cc_start: 0.7616 (m-10) cc_final: 0.7190 (m-10) REVERT: K 93 GLN cc_start: 0.8228 (tp40) cc_final: 0.7999 (tp-100) REVERT: K 213 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.6098 (mt) outliers start: 27 outliers final: 21 residues processed: 114 average time/residue: 0.3140 time to fit residues: 50.2833 Evaluate side-chains 114 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 177 CYS Chi-restraints excluded: chain K residue 184 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 232 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15264 Z= 0.244 Angle : 0.633 26.884 21903 Z= 0.352 Chirality : 0.054 2.006 2495 Planarity : 0.005 0.107 1751 Dihedral : 29.402 174.074 4416 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.15 % Favored : 95.65 % Rotamer: Outliers : 3.10 % Allowed : 23.97 % Favored : 72.94 % 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: 0.61 (0.27), residues: 1035 helix: 1.85 (0.21), residues: 601 sheet: -3.31 (0.68), residues: 34 loop : -1.57 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 71 HIS 0.006 0.001 HIS A 113 PHE 0.030 0.002 PHE K 64 TYR 0.013 0.002 TYR G 50 ARG 0.006 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: C 59 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7093 (m) REVERT: C 91 GLU cc_start: 0.7883 (tp30) cc_final: 0.7397 (tp30) REVERT: C 92 GLU cc_start: 0.8619 (mp0) cc_final: 0.8279 (mp0) REVERT: D 118 TYR cc_start: 0.8716 (t80) cc_final: 0.8472 (t80) REVERT: E 125 GLN cc_start: 0.8036 (mp10) cc_final: 0.7484 (mp10) REVERT: F 77 LYS cc_start: 0.8811 (mttp) cc_final: 0.8519 (mmtt) REVERT: G 36 LYS cc_start: 0.8571 (tptp) cc_final: 0.8175 (tptp) REVERT: G 91 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7819 (tm-30) REVERT: H 98 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7681 (mm) REVERT: H 110 GLU cc_start: 0.7830 (tt0) cc_final: 0.7575 (tm-30) REVERT: K 5 TYR cc_start: 0.4781 (m-10) cc_final: 0.4399 (m-80) REVERT: K 93 GLN cc_start: 0.8249 (tp40) cc_final: 0.7968 (tp-100) outliers start: 27 outliers final: 19 residues processed: 117 average time/residue: 0.2992 time to fit residues: 49.6657 Evaluate side-chains 110 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 177 CYS Chi-restraints excluded: chain K residue 184 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 15264 Z= 0.372 Angle : 0.684 27.168 21903 Z= 0.380 Chirality : 0.057 1.992 2495 Planarity : 0.005 0.109 1751 Dihedral : 29.617 174.938 4416 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.89 % Favored : 93.91 % Rotamer: Outliers : 3.10 % Allowed : 24.31 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1035 helix: 1.59 (0.21), residues: 597 sheet: -3.32 (0.64), residues: 40 loop : -1.60 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 71 HIS 0.007 0.001 HIS A 113 PHE 0.031 0.002 PHE K 64 TYR 0.013 0.002 TYR G 50 ARG 0.006 0.001 ARG D 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: C 59 THR cc_start: 0.7763 (OUTLIER) cc_final: 0.7504 (t) REVERT: C 91 GLU cc_start: 0.7961 (tp30) cc_final: 0.7474 (tp30) REVERT: C 92 GLU cc_start: 0.8635 (mp0) cc_final: 0.8302 (mp0) REVERT: D 118 TYR cc_start: 0.8733 (t80) cc_final: 0.8495 (t80) REVERT: E 125 GLN cc_start: 0.8026 (mp10) cc_final: 0.7487 (mp10) REVERT: F 77 LYS cc_start: 0.8794 (mttp) cc_final: 0.8534 (mmtt) REVERT: G 36 LYS cc_start: 0.8529 (tptp) cc_final: 0.8140 (tppt) REVERT: G 91 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7731 (tm-30) REVERT: H 98 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7643 (mm) REVERT: H 110 GLU cc_start: 0.7845 (tt0) cc_final: 0.7556 (tm-30) REVERT: K 93 GLN cc_start: 0.8207 (tp40) cc_final: 0.7957 (tp-100) REVERT: K 232 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7874 (mtt180) outliers start: 27 outliers final: 21 residues processed: 115 average time/residue: 0.3194 time to fit residues: 51.8412 Evaluate side-chains 113 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 177 CYS Chi-restraints excluded: chain K residue 184 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 232 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 102 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 HIS ** 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 = 0.3920 r_free = 0.3920 target = 0.078148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.058545 restraints weight = 64279.260| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.80 r_work: 0.3264 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 15264 Z= 0.234 Angle : 0.631 26.883 21903 Z= 0.350 Chirality : 0.054 2.003 2495 Planarity : 0.005 0.107 1751 Dihedral : 29.368 173.924 4416 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.35 % Favored : 95.46 % Rotamer: Outliers : 2.75 % Allowed : 25.00 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1035 helix: 1.91 (0.21), residues: 601 sheet: -3.19 (0.71), residues: 34 loop : -1.50 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 71 HIS 0.006 0.001 HIS A 113 PHE 0.025 0.002 PHE K 64 TYR 0.013 0.002 TYR G 50 ARG 0.006 0.000 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2702.85 seconds wall clock time: 49 minutes 28.39 seconds (2968.39 seconds total)