Starting phenix.real_space_refine on Sun Jan 19 17:00:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dby_46728/01_2025/9dby_46728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dby_46728/01_2025/9dby_46728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dby_46728/01_2025/9dby_46728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dby_46728/01_2025/9dby_46728.map" model { file = "/net/cci-nas-00/data/ceres_data/9dby_46728/01_2025/9dby_46728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dby_46728/01_2025/9dby_46728.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.008 sd= 0.052 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 5 6.06 5 P 296 5.49 5 S 35 5.16 5 C 8103 2.51 5 N 2666 2.21 5 O 3263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14368 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 658 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 668 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 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: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3054 Classifications: {'DNA': 148} Link IDs: {'rna3p': 147} Chain: "J" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3014 Classifications: {'DNA': 148} Link IDs: {'rna3p': 147} Chain: "K" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 774 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "L" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 766 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 93} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "M" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 312 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 461 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" 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 12177 SG CYS K 18 44.857 30.580 26.339 1.00145.64 S ATOM 12198 SG CYS K 21 45.062 28.682 23.183 1.00156.22 S ATOM 12336 SG CYS K 39 48.050 28.903 25.456 1.00151.87 S ATOM 12358 SG CYS K 42 46.963 31.939 23.256 1.00142.44 S ATOM 12295 SG CYS K 34 44.556 39.992 36.127 1.00132.24 S ATOM 12439 SG CYS K 53 42.704 39.676 32.791 1.00134.96 S ATOM 12460 SG CYS K 56 40.745 40.482 35.983 1.00131.92 S ATOM 13093 SG CYS L 51 53.439 25.162 52.648 1.00155.30 S ATOM 13114 SG CYS L 54 52.143 22.750 54.897 1.00157.82 S ATOM 13255 SG CYS L 72 49.628 25.167 53.402 1.00134.45 S ATOM 13274 SG CYS L 75 52.103 26.347 56.132 1.00132.62 S ATOM 13209 SG CYS L 67 58.703 34.972 44.952 1.00120.44 S ATOM 13363 SG CYS L 87 59.811 32.804 47.899 1.00132.41 S ATOM 13383 SG CYS L 90 62.338 33.718 45.169 1.00128.23 S ATOM 13638 SG CYS M 27 82.978 95.202 65.944 1.00146.07 S ATOM 13657 SG CYS M 30 86.649 95.173 67.082 1.00146.70 S ATOM 13741 SG CYS M 41 85.854 95.649 63.506 1.00145.31 S ATOM 13761 SG CYS M 44 85.287 92.274 64.927 1.00149.57 S Time building chain proxies: 8.05, per 1000 atoms: 0.56 Number of scatterers: 14368 At special positions: 0 Unit cell: (124.499, 119.086, 119.086, 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 5 29.99 S 35 16.00 P 296 15.00 O 3263 8.00 N 2666 7.00 C 8103 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: 3.66 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 21 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 18 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 42 " pdb=" ZN K 402 " pdb="ZN ZN K 402 " - pdb=" ND1 HIS K 36 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 34 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 56 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 53 " pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 54 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 72 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 75 " pdb=" ZN L 402 " pdb="ZN ZN L 402 " - pdb=" ND1 HIS L 69 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 87 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 67 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 90 " pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 41 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 30 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 44 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 27 " Number of angles added : 24 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 59.1% alpha, 5.7% beta 148 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 6.68 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.687A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 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 120 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: 3.706A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'K' and resid 9 through 13 Processing helix chain 'K' and resid 40 through 48 removed outlier: 3.653A pdb=" N GLU K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 67 Processing helix chain 'K' and resid 72 through 83 Processing helix chain 'K' and resid 85 through 99 Processing helix chain 'L' and resid 45 through 50 Processing helix chain 'L' and resid 73 through 83 Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'L' and resid 103 through 114 Processing helix chain 'N' and resid 22 through 35 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 55 through 60 removed outlier: 3.710A pdb=" N TYR N 59 " --> pdb=" O THR N 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.862A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.266A pdb=" N ARG C 42 " --> 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.866A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.735A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.354A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 5 through 8 Processing sheet with id=AB3, first strand: chain 'K' and resid 36 through 39 Processing sheet with id=AB4, first strand: chain 'L' and resid 70 through 72 Processing sheet with id=AB5, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB6, first strand: chain 'N' and resid 12 through 16 removed outlier: 7.709A pdb=" N GLN N 2 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N LEU N 67 " --> pdb=" O GLN N 2 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU N 69 " --> pdb=" O PHE N 4 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU N 71 " --> pdb=" O LYS N 6 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 379 hydrogen bonds 758 hydrogen bond angles 0 basepair planarities 148 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 5.07 Time building geometry restraints manager: 4.21 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: 3424 1.34 - 1.46: 4344 1.46 - 1.58: 6811 1.58 - 1.70: 590 1.70 - 1.82: 49 Bond restraints: 15218 Sorted by residual: bond pdb=" N ILE K 26 " pdb=" CA ILE K 26 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.17e-02 7.31e+03 9.59e+00 bond pdb=" N ILE C 62 " pdb=" CA ILE C 62 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 8.70e+00 bond pdb=" N VAL F 21 " pdb=" CA VAL F 21 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.29e-02 6.01e+03 8.21e+00 bond pdb=" N VAL B 21 " pdb=" CA VAL B 21 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.24e-02 6.50e+03 7.97e+00 bond pdb=" N ILE F 26 " pdb=" CA ILE F 26 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.30e-02 5.92e+03 6.98e+00 ... (remaining 15213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 21477 2.17 - 4.33: 347 4.33 - 6.50: 38 6.50 - 8.67: 6 8.67 - 10.83: 1 Bond angle restraints: 21869 Sorted by residual: angle pdb=" N GLN B 27 " pdb=" CA GLN B 27 " pdb=" C GLN B 27 " ideal model delta sigma weight residual 114.64 103.81 10.83 1.52e+00 4.33e-01 5.08e+01 angle pdb=" N ASN G 73 " pdb=" CA ASN G 73 " pdb=" C ASN G 73 " ideal model delta sigma weight residual 113.28 107.16 6.12 1.22e+00 6.72e-01 2.52e+01 angle pdb=" N LYS C 74 " pdb=" CA LYS C 74 " pdb=" C LYS C 74 " ideal model delta sigma weight residual 112.58 107.97 4.61 1.22e+00 6.72e-01 1.43e+01 angle pdb=" N ASN F 25 " pdb=" CA ASN F 25 " pdb=" C ASN F 25 " ideal model delta sigma weight residual 113.23 108.64 4.59 1.24e+00 6.50e-01 1.37e+01 angle pdb=" N ASN C 73 " pdb=" CA ASN C 73 " pdb=" C ASN C 73 " ideal model delta sigma weight residual 113.19 108.87 4.32 1.19e+00 7.06e-01 1.32e+01 ... (remaining 21864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.53: 6381 26.53 - 53.07: 1695 53.07 - 79.60: 317 79.60 - 106.14: 2 106.14 - 132.67: 2 Dihedral angle restraints: 8397 sinusoidal: 5245 harmonic: 3152 Sorted by residual: dihedral pdb=" CA ILE B 26 " pdb=" C ILE B 26 " pdb=" N GLN B 27 " pdb=" CA GLN B 27 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" C4' DC I 36 " pdb=" C3' DC I 36 " pdb=" O3' DC I 36 " pdb=" P DT I 37 " ideal model delta sinusoidal sigma weight residual 220.00 87.33 132.67 1 3.50e+01 8.16e-04 1.31e+01 ... (remaining 8394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2496 0.109 - 0.218: 32 0.218 - 0.327: 1 0.327 - 0.436: 0 0.436 - 0.545: 6 Chirality restraints: 2535 Sorted by residual: chirality pdb=" P DT I 35 " pdb=" OP1 DT I 35 " pdb=" OP2 DT I 35 " pdb=" O5' DT I 35 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.55 2.00e-01 2.50e+01 7.43e+00 chirality pdb=" P DA J 151 " pdb=" OP1 DA J 151 " pdb=" OP2 DA J 151 " pdb=" O5' DA J 151 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" P DT I 37 " pdb=" OP1 DT I 37 " pdb=" OP2 DT I 37 " pdb=" O5' DT I 37 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.87e+00 ... (remaining 2532 not shown) Planarity restraints: 1744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 99 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO D 100 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 99 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO H 100 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL K 83 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO K 84 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO K 84 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 84 " 0.027 5.00e-02 4.00e+02 ... (remaining 1741 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2456 2.78 - 3.31: 12479 3.31 - 3.84: 26673 3.84 - 4.37: 31022 4.37 - 4.90: 45681 Nonbonded interactions: 118311 Sorted by model distance: nonbonded pdb=" O LEU L 80 " pdb=" NZ LYS L 85 " model vdw 2.249 3.120 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.284 3.040 nonbonded pdb=" N GLN L 25 " pdb=" OE1 GLN L 25 " model vdw 2.291 3.120 nonbonded pdb=" O GLU N 16 " pdb=" NZ LYS N 29 " model vdw 2.334 3.120 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.337 3.040 ... (remaining 118306 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' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 19 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 117 or resid 119)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 40.400 Find NCS groups from input model: 0.340 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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 : 0.004 0.041 15218 Z= 0.238 Angle : 0.657 10.831 21869 Z= 0.407 Chirality : 0.045 0.545 2535 Planarity : 0.005 0.056 1744 Dihedral : 26.421 132.669 6351 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.23 % Allowed : 16.65 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.26), residues: 1057 helix: 2.53 (0.22), residues: 613 sheet: 1.95 (0.99), residues: 26 loop : -0.32 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 25 HIS 0.002 0.001 HIS D 46 PHE 0.014 0.001 PHE M 32 TYR 0.009 0.001 TYR L 114 ARG 0.008 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 316 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7256 (t0) cc_final: 0.6843 (t0) REVERT: H 73 GLU cc_start: 0.6836 (tp30) cc_final: 0.6495 (tp30) REVERT: L 50 MET cc_start: 0.5528 (mmp) cc_final: 0.4848 (mmt) outliers start: 2 outliers final: 1 residues processed: 316 average time/residue: 1.4128 time to fit residues: 485.7029 Evaluate side-chains 196 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 30.0000 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN K 89 ASN L 29 GLN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.071678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.044664 restraints weight = 70558.719| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.83 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 15218 Z= 0.384 Angle : 0.755 10.182 21869 Z= 0.439 Chirality : 0.044 0.218 2535 Planarity : 0.006 0.066 1744 Dihedral : 28.796 118.825 4422 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.98 % Allowed : 22.51 % Favored : 71.51 % 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: 1.24 (0.25), residues: 1057 helix: 1.70 (0.20), residues: 612 sheet: 1.77 (0.92), residues: 25 loop : -0.52 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 25 HIS 0.008 0.002 HIS H 106 PHE 0.024 0.003 PHE M 39 TYR 0.026 0.003 TYR K 80 ARG 0.020 0.001 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8633 (mmp) REVERT: A 94 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: C 95 LYS cc_start: 0.9520 (tppp) cc_final: 0.9301 (mtpp) REVERT: D 102 GLU cc_start: 0.8793 (mp0) cc_final: 0.8441 (mm-30) REVERT: E 50 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8779 (mt-10) REVERT: E 120 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8656 (mtt) REVERT: G 41 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8172 (tm-30) REVERT: G 64 GLU cc_start: 0.8958 (tp30) cc_final: 0.8648 (tp30) REVERT: G 73 ASN cc_start: 0.8291 (t0) cc_final: 0.8086 (t0) REVERT: G 90 ASP cc_start: 0.8514 (t70) cc_final: 0.8192 (t0) REVERT: H 68 GLU cc_start: 0.8528 (tp30) cc_final: 0.8211 (tp30) REVERT: H 80 TYR cc_start: 0.8590 (m-10) cc_final: 0.8208 (m-10) REVERT: K 17 MET cc_start: 0.9399 (tpp) cc_final: 0.9192 (tpp) REVERT: L 50 MET cc_start: 0.7086 (mmp) cc_final: 0.6414 (mmt) REVERT: L 64 THR cc_start: 0.5773 (p) cc_final: 0.5310 (t) REVERT: L 85 LYS cc_start: 0.4534 (OUTLIER) cc_final: 0.4327 (mppt) REVERT: M 32 PHE cc_start: 0.8556 (t80) cc_final: 0.8217 (t80) outliers start: 51 outliers final: 13 residues processed: 209 average time/residue: 1.5851 time to fit residues: 356.8210 Evaluate side-chains 162 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 85 LYS Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain M residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 104 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 24 GLN D 44 GLN F 25 ASN K 2 HIS K 89 ASN ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.070841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.043731 restraints weight = 69233.530| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.64 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15218 Z= 0.277 Angle : 0.605 8.397 21869 Z= 0.354 Chirality : 0.037 0.157 2535 Planarity : 0.005 0.041 1744 Dihedral : 28.850 112.817 4419 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.75 % Allowed : 26.38 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.26), residues: 1057 helix: 2.28 (0.21), residues: 614 sheet: 2.27 (0.95), residues: 25 loop : -0.46 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 25 HIS 0.006 0.001 HIS L 69 PHE 0.013 0.002 PHE E 67 TYR 0.015 0.002 TYR K 80 ARG 0.009 0.001 ARG K 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8803 (tp30) cc_final: 0.8585 (tp30) REVERT: C 95 LYS cc_start: 0.9543 (tppp) cc_final: 0.9339 (mtpp) REVERT: D 102 GLU cc_start: 0.8750 (mp0) cc_final: 0.8474 (mm-30) REVERT: D 105 LYS cc_start: 0.9000 (mttm) cc_final: 0.8798 (mttm) REVERT: E 93 GLN cc_start: 0.9337 (OUTLIER) cc_final: 0.9060 (mt0) REVERT: E 97 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8493 (mp0) REVERT: E 120 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8698 (mtt) REVERT: G 41 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8043 (tm-30) REVERT: G 90 ASP cc_start: 0.8527 (t70) cc_final: 0.8053 (t0) REVERT: H 68 GLU cc_start: 0.8561 (tp30) cc_final: 0.8240 (tp30) REVERT: H 90 GLU cc_start: 0.8769 (mp0) cc_final: 0.8516 (mp0) REVERT: K 17 MET cc_start: 0.9342 (tpp) cc_final: 0.9123 (tpp) REVERT: L 50 MET cc_start: 0.6743 (mmp) cc_final: 0.6014 (mmt) REVERT: M 32 PHE cc_start: 0.8581 (t80) cc_final: 0.8314 (t80) outliers start: 32 outliers final: 6 residues processed: 172 average time/residue: 1.6233 time to fit residues: 301.6886 Evaluate side-chains 156 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain M residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 93 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 44 GLN H 46 HIS ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.069189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.041807 restraints weight = 68369.883| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.80 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.7348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15218 Z= 0.358 Angle : 0.624 8.554 21869 Z= 0.367 Chirality : 0.039 0.204 2535 Planarity : 0.005 0.052 1744 Dihedral : 28.876 101.636 4419 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.70 % Allowed : 27.20 % Favored : 70.11 % 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: 1.83 (0.25), residues: 1057 helix: 2.26 (0.21), residues: 618 sheet: 2.48 (0.99), residues: 25 loop : -0.50 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP M 25 HIS 0.008 0.001 HIS L 69 PHE 0.016 0.002 PHE M 32 TYR 0.017 0.002 TYR K 80 ARG 0.014 0.001 ARG M 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ILE cc_start: 0.9696 (OUTLIER) cc_final: 0.9382 (mm) REVERT: C 91 GLU cc_start: 0.8822 (tp30) cc_final: 0.8562 (tp30) REVERT: C 95 LYS cc_start: 0.9571 (tppp) cc_final: 0.9221 (mtpp) REVERT: E 76 GLN cc_start: 0.8957 (tp40) cc_final: 0.8425 (tp-100) REVERT: G 41 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7947 (tm-30) REVERT: G 56 GLU cc_start: 0.9025 (tt0) cc_final: 0.8815 (tt0) REVERT: G 90 ASP cc_start: 0.8697 (t70) cc_final: 0.8390 (t0) REVERT: G 110 ASN cc_start: 0.9228 (t0) cc_final: 0.8776 (t0) REVERT: H 31 LYS cc_start: 0.9029 (pmmt) cc_final: 0.8701 (pmtt) REVERT: H 68 GLU cc_start: 0.8544 (tp30) cc_final: 0.8303 (tp30) REVERT: H 90 GLU cc_start: 0.8914 (mp0) cc_final: 0.8511 (mp0) REVERT: K 17 MET cc_start: 0.9345 (tpp) cc_final: 0.9042 (tpp) REVERT: K 24 TYR cc_start: 0.8737 (m-10) cc_final: 0.8410 (m-80) REVERT: M 32 PHE cc_start: 0.8520 (t80) cc_final: 0.8246 (t80) outliers start: 23 outliers final: 6 residues processed: 171 average time/residue: 1.7799 time to fit residues: 325.6920 Evaluate side-chains 149 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain L residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 94 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 46 optimal weight: 0.0020 chunk 51 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 125 GLN K 59 GLN ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.070254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.043433 restraints weight = 68936.934| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.72 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15218 Z= 0.198 Angle : 0.570 9.659 21869 Z= 0.333 Chirality : 0.035 0.244 2535 Planarity : 0.004 0.038 1744 Dihedral : 28.620 97.460 4419 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.23 % Allowed : 27.90 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.26), residues: 1057 helix: 2.56 (0.21), residues: 617 sheet: 2.78 (1.02), residues: 25 loop : -0.41 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 25 HIS 0.005 0.001 HIS B 75 PHE 0.012 0.001 PHE M 32 TYR 0.009 0.001 TYR D 39 ARG 0.018 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8787 (tp30) cc_final: 0.8539 (tp30) REVERT: C 95 LYS cc_start: 0.9571 (tppp) cc_final: 0.9291 (mtpp) REVERT: E 76 GLN cc_start: 0.8927 (tp40) cc_final: 0.8673 (tm-30) REVERT: G 41 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8004 (tm-30) REVERT: G 56 GLU cc_start: 0.8987 (tt0) cc_final: 0.8739 (tt0) REVERT: G 90 ASP cc_start: 0.8632 (t70) cc_final: 0.8149 (t0) REVERT: G 110 ASN cc_start: 0.9206 (t0) cc_final: 0.8770 (t0) REVERT: H 68 GLU cc_start: 0.8559 (tp30) cc_final: 0.8282 (tp30) REVERT: H 90 GLU cc_start: 0.8907 (mp0) cc_final: 0.8473 (mp0) REVERT: K 24 TYR cc_start: 0.8782 (m-10) cc_final: 0.8534 (m-80) REVERT: K 59 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: L 63 THR cc_start: 0.7933 (m) cc_final: 0.7593 (p) REVERT: M 32 PHE cc_start: 0.8664 (t80) cc_final: 0.8424 (t80) outliers start: 19 outliers final: 6 residues processed: 178 average time/residue: 1.5566 time to fit residues: 298.8469 Evaluate side-chains 161 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 59 GLN Chi-restraints excluded: chain L residue 64 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 70 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN F 25 ASN ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.070645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.043939 restraints weight = 69751.991| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.88 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15218 Z= 0.182 Angle : 0.580 9.237 21869 Z= 0.333 Chirality : 0.035 0.255 2535 Planarity : 0.004 0.039 1744 Dihedral : 28.487 93.211 4419 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.52 % Allowed : 28.72 % Favored : 69.75 % 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: 2.28 (0.26), residues: 1057 helix: 2.69 (0.21), residues: 614 sheet: 2.85 (1.03), residues: 25 loop : -0.41 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 25 HIS 0.005 0.001 HIS B 75 PHE 0.016 0.001 PHE K 38 TYR 0.011 0.001 TYR L 22 ARG 0.010 0.001 ARG M 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.8934 (tp40) cc_final: 0.8670 (tm-30) REVERT: G 41 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8018 (tm-30) REVERT: G 56 GLU cc_start: 0.8991 (tt0) cc_final: 0.8734 (tt0) REVERT: G 90 ASP cc_start: 0.8589 (t70) cc_final: 0.8153 (t0) REVERT: G 110 ASN cc_start: 0.9226 (t0) cc_final: 0.8792 (t0) REVERT: H 31 LYS cc_start: 0.8925 (pmmt) cc_final: 0.8674 (pmtt) REVERT: H 68 GLU cc_start: 0.8572 (tp30) cc_final: 0.8279 (tp30) REVERT: H 90 GLU cc_start: 0.8954 (mp0) cc_final: 0.8453 (mp0) REVERT: H 113 LYS cc_start: 0.9298 (ttpp) cc_final: 0.9013 (ttmm) REVERT: K 13 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8310 (m110) REVERT: K 17 MET cc_start: 0.9493 (mmm) cc_final: 0.8876 (tpp) REVERT: K 24 TYR cc_start: 0.8831 (m-10) cc_final: 0.8316 (m-80) REVERT: K 43 ILE cc_start: 0.8630 (tp) cc_final: 0.8302 (mt) REVERT: L 57 MET cc_start: 0.8432 (ppp) cc_final: 0.8014 (mpt) REVERT: M 32 PHE cc_start: 0.8598 (t80) cc_final: 0.8364 (t80) REVERT: M 33 ARG cc_start: 0.8720 (mmm160) cc_final: 0.8515 (mmm160) outliers start: 13 outliers final: 5 residues processed: 172 average time/residue: 1.5802 time to fit residues: 293.3814 Evaluate side-chains 160 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 154 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain L residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 87 optimal weight: 10.0000 chunk 104 optimal weight: 0.3980 chunk 26 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 101 optimal weight: 30.0000 chunk 76 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.068473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.041169 restraints weight = 68601.520| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 3.84 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.7906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 15218 Z= 0.400 Angle : 0.642 10.109 21869 Z= 0.372 Chirality : 0.040 0.214 2535 Planarity : 0.005 0.038 1744 Dihedral : 28.692 88.787 4419 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.52 % Allowed : 29.07 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.26), residues: 1057 helix: 2.44 (0.21), residues: 618 sheet: 2.90 (1.04), residues: 25 loop : -0.55 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 25 HIS 0.005 0.001 HIS B 75 PHE 0.017 0.002 PHE K 38 TYR 0.014 0.002 TYR K 52 ARG 0.020 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8559 (mm-30) REVERT: E 76 GLN cc_start: 0.9023 (tp40) cc_final: 0.8482 (tp-100) REVERT: G 41 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8043 (tm-30) REVERT: G 90 ASP cc_start: 0.8791 (t70) cc_final: 0.8274 (t0) REVERT: G 110 ASN cc_start: 0.9213 (t0) cc_final: 0.8766 (t0) REVERT: H 68 GLU cc_start: 0.8607 (tp30) cc_final: 0.8368 (tp30) REVERT: H 113 LYS cc_start: 0.9302 (ttpp) cc_final: 0.9031 (ttmm) REVERT: K 13 ASN cc_start: 0.9064 (OUTLIER) cc_final: 0.8308 (m110) REVERT: K 17 MET cc_start: 0.9454 (mmm) cc_final: 0.8924 (tpp) REVERT: K 24 TYR cc_start: 0.8851 (m-10) cc_final: 0.8410 (m-80) REVERT: K 59 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8138 (tm-30) REVERT: M 32 PHE cc_start: 0.8605 (t80) cc_final: 0.8102 (t80) REVERT: M 33 ARG cc_start: 0.8739 (mmm160) cc_final: 0.8539 (mmm160) outliers start: 13 outliers final: 5 residues processed: 163 average time/residue: 1.5795 time to fit residues: 277.5782 Evaluate side-chains 155 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain L residue 64 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 49 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 0.0040 chunk 16 optimal weight: 0.6980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 GLN ** 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 = 0.3616 r_free = 0.3616 target = 0.069675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.042689 restraints weight = 68651.540| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.91 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.7925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15218 Z= 0.188 Angle : 0.619 11.514 21869 Z= 0.351 Chirality : 0.037 0.267 2535 Planarity : 0.005 0.059 1744 Dihedral : 28.651 87.106 4419 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.52 % Allowed : 29.66 % Favored : 68.82 % 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: 2.13 (0.26), residues: 1057 helix: 2.57 (0.21), residues: 623 sheet: 2.84 (1.06), residues: 25 loop : -0.57 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP M 25 HIS 0.004 0.001 HIS B 75 PHE 0.022 0.002 PHE K 38 TYR 0.011 0.001 TYR L 22 ARG 0.011 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.8946 (tp40) cc_final: 0.8678 (tm-30) REVERT: G 41 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8026 (tm-30) REVERT: G 90 ASP cc_start: 0.8662 (t70) cc_final: 0.8139 (t0) REVERT: G 110 ASN cc_start: 0.9172 (t0) cc_final: 0.8735 (t0) REVERT: H 68 GLU cc_start: 0.8550 (tp30) cc_final: 0.8288 (tp30) REVERT: H 90 GLU cc_start: 0.8890 (mp0) cc_final: 0.8475 (mp0) REVERT: H 113 LYS cc_start: 0.9300 (ttpp) cc_final: 0.9027 (ttmm) REVERT: K 13 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8371 (m110) REVERT: K 17 MET cc_start: 0.9473 (mmm) cc_final: 0.8936 (tpp) REVERT: K 24 TYR cc_start: 0.8842 (m-10) cc_final: 0.8409 (m-80) REVERT: K 59 GLN cc_start: 0.8278 (tm-30) cc_final: 0.8063 (tm-30) REVERT: L 57 MET cc_start: 0.8268 (ppp) cc_final: 0.8034 (mpt) outliers start: 13 outliers final: 10 residues processed: 168 average time/residue: 1.5619 time to fit residues: 282.6783 Evaluate side-chains 166 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 105 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 102 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 62 optimal weight: 0.0570 chunk 72 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 79 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 GLN ** 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 = 0.3608 r_free = 0.3608 target = 0.069269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.042343 restraints weight = 68109.749| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.83 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.8004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15218 Z= 0.258 Angle : 0.626 10.684 21869 Z= 0.355 Chirality : 0.037 0.245 2535 Planarity : 0.004 0.039 1744 Dihedral : 28.524 80.331 4419 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.41 % Allowed : 30.36 % Favored : 68.23 % 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: 2.12 (0.26), residues: 1057 helix: 2.65 (0.21), residues: 617 sheet: 2.74 (1.07), residues: 25 loop : -0.66 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP M 25 HIS 0.005 0.001 HIS B 75 PHE 0.026 0.002 PHE K 38 TYR 0.013 0.001 TYR K 52 ARG 0.012 0.001 ARG M 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.8636 (mtp85) REVERT: E 76 GLN cc_start: 0.8981 (tp40) cc_final: 0.8696 (tm-30) REVERT: G 41 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8051 (tm-30) REVERT: G 90 ASP cc_start: 0.8635 (t70) cc_final: 0.8136 (t0) REVERT: G 110 ASN cc_start: 0.9222 (t0) cc_final: 0.8787 (t0) REVERT: H 68 GLU cc_start: 0.8578 (tp30) cc_final: 0.8319 (tp30) REVERT: H 90 GLU cc_start: 0.8935 (mp0) cc_final: 0.8531 (mp0) REVERT: H 113 LYS cc_start: 0.9301 (ttpp) cc_final: 0.9023 (ttmm) REVERT: K 13 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8318 (m110) REVERT: K 17 MET cc_start: 0.9466 (mmm) cc_final: 0.8933 (tpp) REVERT: K 24 TYR cc_start: 0.8858 (m-10) cc_final: 0.8412 (m-80) REVERT: K 46 TYR cc_start: 0.8261 (t80) cc_final: 0.7785 (t80) REVERT: K 47 LEU cc_start: 0.8432 (pp) cc_final: 0.7987 (mp) REVERT: K 59 GLN cc_start: 0.8320 (tm-30) cc_final: 0.8105 (tm-30) outliers start: 12 outliers final: 8 residues processed: 167 average time/residue: 1.6483 time to fit residues: 296.2005 Evaluate side-chains 163 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 105 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 109 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** C 73 ASN ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.068321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.041240 restraints weight = 67794.827| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.80 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.8170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15218 Z= 0.372 Angle : 0.660 13.865 21869 Z= 0.376 Chirality : 0.040 0.224 2535 Planarity : 0.005 0.043 1744 Dihedral : 28.615 80.141 4419 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.52 % Allowed : 30.01 % Favored : 68.46 % 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: 1.90 (0.26), residues: 1057 helix: 2.42 (0.21), residues: 625 sheet: 2.71 (1.06), residues: 25 loop : -0.75 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP M 25 HIS 0.005 0.001 HIS L 69 PHE 0.027 0.002 PHE K 38 TYR 0.013 0.002 TYR L 22 ARG 0.013 0.001 ARG M 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.8688 (mtp85) REVERT: E 76 GLN cc_start: 0.9012 (tp40) cc_final: 0.8488 (tp-100) REVERT: E 97 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8631 (mp0) REVERT: G 41 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8129 (tm-30) REVERT: G 90 ASP cc_start: 0.8756 (t70) cc_final: 0.8199 (t0) REVERT: G 110 ASN cc_start: 0.9210 (t0) cc_final: 0.8769 (t0) REVERT: H 68 GLU cc_start: 0.8603 (tp30) cc_final: 0.8364 (tp30) REVERT: H 90 GLU cc_start: 0.8952 (mp0) cc_final: 0.8544 (mp0) REVERT: H 113 LYS cc_start: 0.9289 (ttpp) cc_final: 0.9013 (ttmm) REVERT: K 17 MET cc_start: 0.9460 (mmm) cc_final: 0.9104 (tpp) REVERT: K 24 TYR cc_start: 0.8829 (m-10) cc_final: 0.8483 (m-80) REVERT: K 46 TYR cc_start: 0.8396 (t80) cc_final: 0.7918 (t80) REVERT: K 47 LEU cc_start: 0.8542 (pp) cc_final: 0.8150 (mp) REVERT: K 59 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8180 (tm-30) outliers start: 13 outliers final: 10 residues processed: 166 average time/residue: 1.6443 time to fit residues: 293.1756 Evaluate side-chains 161 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 101 ARG Chi-restraints excluded: chain L residue 105 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 96 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 GLN ** 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 = 0.3591 r_free = 0.3591 target = 0.068761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.041755 restraints weight = 68122.939| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 3.76 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.8199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15218 Z= 0.271 Angle : 0.651 12.838 21869 Z= 0.367 Chirality : 0.038 0.244 2535 Planarity : 0.005 0.060 1744 Dihedral : 28.637 80.363 4419 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.52 % Allowed : 30.36 % Favored : 68.11 % 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: 1.90 (0.26), residues: 1057 helix: 2.45 (0.21), residues: 625 sheet: 2.62 (1.06), residues: 25 loop : -0.80 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP M 25 HIS 0.005 0.001 HIS B 75 PHE 0.025 0.002 PHE K 38 TYR 0.013 0.001 TYR D 39 ARG 0.013 0.001 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9071.54 seconds wall clock time: 162 minutes 13.36 seconds (9733.36 seconds total)