Starting phenix.real_space_refine on Sun May 11 02:38:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g07_29648/05_2025/8g07_29648.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g07_29648/05_2025/8g07_29648.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/8g07_29648/05_2025/8g07_29648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g07_29648/05_2025/8g07_29648.map" model { file = "/net/cci-nas-00/data/ceres_data/8g07_29648/05_2025/8g07_29648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g07_29648/05_2025/8g07_29648.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= 0.014 sd= 0.169 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 4978 2.51 5 N 1212 2.21 5 O 1250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7467 Number of models: 1 Model: "" Number of chains: 13 Chain: "1" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "2" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 554 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "3" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} 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: "4" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} 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: "5" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} 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: "6" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} 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: "7" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} 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: "8" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "9" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} 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: "a" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1808 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "b" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 312 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 37} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "d" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 295 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 37} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "9" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'SQC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.57, per 1000 atoms: 0.75 Number of scatterers: 7467 At special positions: 0 Unit cell: (89.61, 76.22, 84.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1250 8.00 N 1212 7.00 C 4978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 88.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain '1' and resid 5 through 46 Processing helix chain '1' and resid 48 through 81 removed outlier: 4.269A pdb=" N ARG 1 52 " --> pdb=" O GLU 1 48 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE 1 54 " --> pdb=" O GLN 1 50 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR 1 55 " --> pdb=" O GLY 1 51 " (cutoff:3.500A) Proline residue: 1 56 - end of helix removed outlier: 3.763A pdb=" N ALA 1 67 " --> pdb=" O LEU 1 63 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR 1 68 " --> pdb=" O VAL 1 64 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 46 Processing helix chain '2' and resid 49 through 81 removed outlier: 4.394A pdb=" N THR 2 55 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Proline residue: 2 56 - end of helix Processing helix chain '3' and resid 6 through 46 Processing helix chain '3' and resid 49 through 80 removed outlier: 4.410A pdb=" N THR 3 55 " --> pdb=" O GLY 3 51 " (cutoff:3.500A) Proline residue: 3 56 - end of helix Processing helix chain '4' and resid 6 through 46 Processing helix chain '4' and resid 49 through 81 removed outlier: 3.670A pdb=" N PHE 4 54 " --> pdb=" O GLN 4 50 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR 4 55 " --> pdb=" O GLY 4 51 " (cutoff:3.500A) Proline residue: 4 56 - end of helix Processing helix chain '5' and resid 6 through 46 Processing helix chain '5' and resid 49 through 80 removed outlier: 3.847A pdb=" N THR 5 55 " --> pdb=" O GLY 5 51 " (cutoff:3.500A) Proline residue: 5 56 - end of helix Processing helix chain '6' and resid 6 through 46 Processing helix chain '6' and resid 49 through 80 removed outlier: 4.501A pdb=" N THR 6 55 " --> pdb=" O GLY 6 51 " (cutoff:3.500A) Proline residue: 6 56 - end of helix Processing helix chain '7' and resid 6 through 46 Processing helix chain '7' and resid 48 through 80 removed outlier: 4.102A pdb=" N ARG 7 52 " --> pdb=" O GLU 7 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE 7 54 " --> pdb=" O GLN 7 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR 7 55 " --> pdb=" O GLY 7 51 " (cutoff:3.500A) Proline residue: 7 56 - end of helix Processing helix chain '8' and resid 6 through 46 Processing helix chain '8' and resid 49 through 80 removed outlier: 4.025A pdb=" N THR 8 55 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) Proline residue: 8 56 - end of helix Processing helix chain '9' and resid 6 through 46 Processing helix chain '9' and resid 48 through 53 removed outlier: 4.205A pdb=" N ARG 9 52 " --> pdb=" O GLU 9 48 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 80 removed outlier: 3.775A pdb=" N ALA 9 67 " --> pdb=" O LEU 9 63 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR 9 68 " --> pdb=" O VAL 9 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE 9 80 " --> pdb=" O ALA 9 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 52 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.576A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR a 95 " --> pdb=" O PRO a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.745A pdb=" N ILE a 160 " --> pdb=" O VAL a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 204 removed outlier: 3.634A pdb=" N VAL a 176 " --> pdb=" O PRO a 172 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU a 177 " --> pdb=" O ILE a 173 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 3.828A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 5.561A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix Processing helix chain 'b' and resid 29 through 49 Processing helix chain 'b' and resid 49 through 64 removed outlier: 3.565A pdb=" N LEU b 64 " --> pdb=" O ARG b 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 40 Processing sheet with id=AA1, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'a' and resid 112 through 114 746 hydrogen bonds defined for protein. 2229 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1165 1.28 - 1.41: 1918 1.41 - 1.54: 4487 1.54 - 1.68: 10 1.68 - 1.81: 53 Bond restraints: 7633 Sorted by residual: bond pdb=" C PHE a 221 " pdb=" O PHE a 221 " ideal model delta sigma weight residual 1.237 1.144 0.093 1.17e-02 7.31e+03 6.28e+01 bond pdb=" C ASN 5 6 " pdb=" O ASN 5 6 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.17e-02 7.31e+03 6.03e+01 bond pdb=" C16 SQC 9 601 " pdb=" N17 SQC 9 601 " ideal model delta sigma weight residual 1.320 1.459 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" N GLN 4 46 " pdb=" CA GLN 4 46 " ideal model delta sigma weight residual 1.464 1.390 0.073 1.09e-02 8.42e+03 4.50e+01 bond pdb=" C ASN 4 6 " pdb=" O ASN 4 6 " ideal model delta sigma weight residual 1.237 1.159 0.078 1.17e-02 7.31e+03 4.45e+01 ... (remaining 7628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 10103 1.90 - 3.81: 210 3.81 - 5.71: 53 5.71 - 7.61: 10 7.61 - 9.51: 2 Bond angle restraints: 10378 Sorted by residual: angle pdb=" C GLN 6 46 " pdb=" N PRO 6 47 " pdb=" CA PRO 6 47 " ideal model delta sigma weight residual 119.84 111.35 8.49 1.25e+00 6.40e-01 4.61e+01 angle pdb=" N THR d 28 " pdb=" CA THR d 28 " pdb=" C THR d 28 " ideal model delta sigma weight residual 110.97 104.31 6.66 1.09e+00 8.42e-01 3.73e+01 angle pdb=" N ALA 9 66 " pdb=" CA ALA 9 66 " pdb=" C ALA 9 66 " ideal model delta sigma weight residual 110.97 104.55 6.42 1.09e+00 8.42e-01 3.46e+01 angle pdb=" N VAL d 26 " pdb=" CA VAL d 26 " pdb=" C VAL d 26 " ideal model delta sigma weight residual 110.62 104.79 5.83 1.02e+00 9.61e-01 3.27e+01 angle pdb=" C GLN 4 46 " pdb=" N PRO 4 47 " pdb=" CA PRO 4 47 " ideal model delta sigma weight residual 119.56 124.73 -5.17 1.02e+00 9.61e-01 2.57e+01 ... (remaining 10373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 3821 15.84 - 31.69: 372 31.69 - 47.53: 73 47.53 - 63.37: 26 63.37 - 79.22: 9 Dihedral angle restraints: 4301 sinusoidal: 1496 harmonic: 2805 Sorted by residual: dihedral pdb=" C ALA 9 66 " pdb=" N ALA 9 66 " pdb=" CA ALA 9 66 " pdb=" CB ALA 9 66 " ideal model delta harmonic sigma weight residual -122.60 -111.73 -10.87 0 2.50e+00 1.60e-01 1.89e+01 dihedral pdb=" CA PHE 9 80 " pdb=" C PHE 9 80 " pdb=" N ALA 9 81 " pdb=" CA ALA 9 81 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" N GLN 4 46 " pdb=" C GLN 4 46 " pdb=" CA GLN 4 46 " pdb=" CB GLN 4 46 " ideal model delta harmonic sigma weight residual 122.80 113.21 9.59 0 2.50e+00 1.60e-01 1.47e+01 ... (remaining 4298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 949 0.048 - 0.096: 241 0.096 - 0.144: 36 0.144 - 0.192: 8 0.192 - 0.240: 1 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CB VAL 9 64 " pdb=" CA VAL 9 64 " pdb=" CG1 VAL 9 64 " pdb=" CG2 VAL 9 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA LEU 8 72 " pdb=" N LEU 8 72 " pdb=" C LEU 8 72 " pdb=" CB LEU 8 72 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA PRO 6 47 " pdb=" N PRO 6 47 " pdb=" C PRO 6 47 " pdb=" CB PRO 6 47 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 1232 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA 3 76 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ALA 3 76 " -0.065 2.00e-02 2.50e+03 pdb=" O ALA 3 76 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU 3 77 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY a 197 " -0.013 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" C GLY a 197 " 0.043 2.00e-02 2.50e+03 pdb=" O GLY a 197 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE a 198 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 4 69 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C PHE 4 69 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE 4 69 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE 4 70 " 0.014 2.00e-02 2.50e+03 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1784 2.78 - 3.31: 8206 3.31 - 3.84: 13861 3.84 - 4.37: 16310 4.37 - 4.90: 28042 Nonbonded interactions: 68203 Sorted by model distance: nonbonded pdb=" OG SER a 55 " pdb=" OE1 GLU b 59 " model vdw 2.253 3.040 nonbonded pdb=" O GLN a 72 " pdb=" OE1 GLN a 76 " model vdw 2.299 3.040 nonbonded pdb=" O PHE a 99 " pdb=" OG SER a 103 " model vdw 2.304 3.040 nonbonded pdb=" OD1 ASP a 30 " pdb=" N THR a 31 " model vdw 2.314 3.120 nonbonded pdb=" O ALA 7 67 " pdb=" OD1 ASN 7 71 " model vdw 2.381 3.040 ... (remaining 68198 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 '1' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) selection = (chain '2' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 85)) selection = (chain '3' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '4' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '5' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '6' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '7' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '8' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) selection = (chain '9' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) } 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: 1.830 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.690 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 : 0.008 0.139 7633 Z= 0.588 Angle : 0.715 9.513 10378 Z= 0.463 Chirality : 0.043 0.240 1235 Planarity : 0.005 0.057 1309 Dihedral : 13.982 79.219 2543 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.15 % Allowed : 2.31 % Favored : 96.54 % Cbeta Deviations : 0.11 % 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: 1.07 (0.27), residues: 1019 helix: 1.07 (0.18), residues: 843 sheet: -1.97 (1.47), residues: 9 loop : -0.67 (0.53), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 PHE 0.012 0.001 PHE 6 74 TYR 0.014 0.001 TYR a 145 ARG 0.007 0.001 ARG 7 52 Details of bonding type rmsd hydrogen bonds : bond 0.14577 ( 746) hydrogen bonds : angle 7.30945 ( 2229) covalent geometry : bond 0.00828 ( 7633) covalent geometry : angle 0.71486 (10378) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.794 Fit side-chains REVERT: 4 21 MET cc_start: 0.7539 (mmm) cc_final: 0.7272 (mmm) REVERT: 4 45 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6860 (tmt170) REVERT: 7 58 PHE cc_start: 0.7971 (m-80) cc_final: 0.7706 (m-80) REVERT: a 73 MET cc_start: 0.7829 (mmt) cc_final: 0.7146 (mmt) REVERT: a 210 ILE cc_start: 0.7473 (mm) cc_final: 0.7261 (mm) outliers start: 8 outliers final: 0 residues processed: 125 average time/residue: 1.0147 time to fit residues: 135.1404 Evaluate side-chains 92 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 45 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 chunk 93 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 6 ASN 7 46 GLN ** 7 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 46 GLN 9 50 GLN ** a 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 215 ASN d 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113599 restraints weight = 8475.523| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.54 r_work: 0.3300 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7633 Z= 0.160 Angle : 0.559 6.379 10378 Z= 0.298 Chirality : 0.041 0.162 1235 Planarity : 0.004 0.040 1309 Dihedral : 5.527 58.105 1110 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.87 % Allowed : 10.09 % Favored : 88.04 % 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: 3.13 (0.26), residues: 1019 helix: 2.44 (0.17), residues: 844 sheet: -1.91 (1.49), residues: 9 loop : 0.37 (0.52), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 48 HIS 0.004 0.001 HIS a 146 PHE 0.020 0.002 PHE 6 74 TYR 0.025 0.001 TYR a 145 ARG 0.007 0.001 ARG 1 52 Details of bonding type rmsd hydrogen bonds : bond 0.05000 ( 746) hydrogen bonds : angle 4.66430 ( 2229) covalent geometry : bond 0.00339 ( 7633) covalent geometry : angle 0.55882 (10378) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.896 Fit side-chains REVERT: 4 45 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.6782 (tpt90) REVERT: a 73 MET cc_start: 0.8412 (mmt) cc_final: 0.7745 (mmt) REVERT: a 75 GLN cc_start: 0.7989 (mt0) cc_final: 0.7724 (mt0) REVERT: a 208 TRP cc_start: 0.8081 (p-90) cc_final: 0.7873 (p-90) REVERT: a 210 ILE cc_start: 0.7353 (mm) cc_final: 0.7054 (tp) outliers start: 13 outliers final: 6 residues processed: 116 average time/residue: 1.1077 time to fit residues: 136.9341 Evaluate side-chains 98 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 6 residue 8 ILE Chi-restraints excluded: chain 8 residue 6 ASN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 71 ASN 7 6 ASN 7 46 GLN 9 50 GLN a 63 GLN a 215 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.110666 restraints weight = 8782.813| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.58 r_work: 0.3255 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7633 Z= 0.182 Angle : 0.546 6.512 10378 Z= 0.291 Chirality : 0.041 0.147 1235 Planarity : 0.004 0.043 1309 Dihedral : 5.557 63.478 1110 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.74 % Allowed : 12.39 % Favored : 84.87 % 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: 3.43 (0.26), residues: 1019 helix: 2.66 (0.17), residues: 844 sheet: -1.90 (1.49), residues: 9 loop : 0.41 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 48 HIS 0.003 0.001 HIS a 146 PHE 0.019 0.002 PHE a 194 TYR 0.024 0.001 TYR a 145 ARG 0.005 0.001 ARG 1 52 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 746) hydrogen bonds : angle 4.48079 ( 2229) covalent geometry : bond 0.00412 ( 7633) covalent geometry : angle 0.54640 (10378) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.744 Fit side-chains REVERT: 2 75 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8223 (tmm) REVERT: 4 45 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6640 (tpt90) REVERT: 6 74 PHE cc_start: 0.8259 (m-80) cc_final: 0.8008 (m-80) REVERT: a 76 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7540 (mp10) REVERT: a 210 ILE cc_start: 0.7298 (mm) cc_final: 0.6944 (tp) REVERT: d 1 MET cc_start: 0.7545 (tpp) cc_final: 0.7151 (tpp) REVERT: d 5 ILE cc_start: 0.7850 (mm) cc_final: 0.7582 (mp) outliers start: 19 outliers final: 6 residues processed: 120 average time/residue: 1.2044 time to fit residues: 153.9236 Evaluate side-chains 106 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 6 residue 72 LEU Chi-restraints excluded: chain 9 residue 21 MET Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 215 ASN Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN 9 50 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.131547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109088 restraints weight = 8784.050| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.55 r_work: 0.3231 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7633 Z= 0.209 Angle : 0.560 6.552 10378 Z= 0.298 Chirality : 0.041 0.165 1235 Planarity : 0.005 0.044 1309 Dihedral : 5.677 67.352 1110 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.75 % Allowed : 12.10 % Favored : 84.15 % 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: 3.31 (0.26), residues: 1019 helix: 2.59 (0.17), residues: 843 sheet: -1.92 (1.48), residues: 9 loop : 0.31 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 48 HIS 0.002 0.001 HIS a 146 PHE 0.018 0.002 PHE a 194 TYR 0.024 0.001 TYR a 145 ARG 0.010 0.001 ARG 2 45 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 746) hydrogen bonds : angle 4.50450 ( 2229) covalent geometry : bond 0.00483 ( 7633) covalent geometry : angle 0.56031 (10378) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.849 Fit side-chains REVERT: 2 21 MET cc_start: 0.8504 (mmm) cc_final: 0.8154 (mmm) REVERT: 2 75 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8207 (tmm) REVERT: 4 45 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6614 (tpt90) REVERT: 5 45 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6883 (ptm160) REVERT: 5 52 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7198 (mtm180) REVERT: 6 74 PHE cc_start: 0.8381 (m-80) cc_final: 0.8065 (m-80) REVERT: a 50 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6546 (ttm170) REVERT: a 73 MET cc_start: 0.8495 (mmt) cc_final: 0.7718 (mmt) REVERT: a 76 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: a 210 ILE cc_start: 0.7246 (mm) cc_final: 0.6853 (tp) REVERT: d 1 MET cc_start: 0.7556 (tpp) cc_final: 0.7132 (tpp) REVERT: d 5 ILE cc_start: 0.7824 (mm) cc_final: 0.7559 (mp) REVERT: d 27 ARG cc_start: 0.6454 (OUTLIER) cc_final: 0.6068 (ttm-80) outliers start: 26 outliers final: 5 residues processed: 116 average time/residue: 1.0283 time to fit residues: 127.4068 Evaluate side-chains 109 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 52 ARG Chi-restraints excluded: chain 8 residue 6 ASN Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 58 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.132851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.110383 restraints weight = 8693.774| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.56 r_work: 0.3255 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7633 Z= 0.170 Angle : 0.527 6.544 10378 Z= 0.282 Chirality : 0.040 0.176 1235 Planarity : 0.004 0.043 1309 Dihedral : 5.609 69.824 1110 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.60 % Allowed : 12.39 % Favored : 84.01 % 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: 3.41 (0.26), residues: 1019 helix: 2.68 (0.17), residues: 842 sheet: -2.06 (1.42), residues: 9 loop : 0.22 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 48 HIS 0.003 0.001 HIS a 146 PHE 0.020 0.002 PHE 1 69 TYR 0.023 0.001 TYR a 145 ARG 0.009 0.001 ARG 1 52 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 746) hydrogen bonds : angle 4.42912 ( 2229) covalent geometry : bond 0.00378 ( 7633) covalent geometry : angle 0.52730 (10378) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.741 Fit side-chains REVERT: 2 75 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8259 (tmm) REVERT: 3 52 ARG cc_start: 0.8712 (ptt-90) cc_final: 0.8418 (ptt-90) REVERT: 4 45 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6620 (tpt90) REVERT: 5 45 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6901 (ptm160) REVERT: 5 52 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7198 (mtm180) REVERT: 6 74 PHE cc_start: 0.8415 (m-80) cc_final: 0.8051 (m-80) REVERT: 7 85 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7516 (mp) REVERT: a 73 MET cc_start: 0.8470 (mmt) cc_final: 0.7645 (mmt) REVERT: a 76 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7431 (mp10) REVERT: a 80 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.7979 (t) REVERT: d 1 MET cc_start: 0.7589 (tpp) cc_final: 0.7185 (tpp) REVERT: d 5 ILE cc_start: 0.7810 (mm) cc_final: 0.7536 (mp) REVERT: d 27 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6380 (ttm-80) outliers start: 25 outliers final: 5 residues processed: 115 average time/residue: 1.0093 time to fit residues: 123.7652 Evaluate side-chains 110 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 52 ARG Chi-restraints excluded: chain 6 residue 72 LEU Chi-restraints excluded: chain 7 residue 85 LEU Chi-restraints excluded: chain 8 residue 6 ASN Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 17 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 82 optimal weight: 0.0050 chunk 86 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN a 28 ASN a 192 ASN a 215 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.133785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111136 restraints weight = 8726.658| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.57 r_work: 0.3262 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7633 Z= 0.159 Angle : 0.520 6.551 10378 Z= 0.277 Chirality : 0.040 0.155 1235 Planarity : 0.004 0.043 1309 Dihedral : 5.563 71.323 1110 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.60 % Allowed : 13.11 % Favored : 83.29 % 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: 3.52 (0.26), residues: 1019 helix: 2.77 (0.17), residues: 842 sheet: -2.06 (1.42), residues: 9 loop : 0.17 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 48 HIS 0.003 0.001 HIS a 146 PHE 0.020 0.002 PHE 1 69 TYR 0.023 0.001 TYR a 145 ARG 0.005 0.000 ARG 1 52 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 746) hydrogen bonds : angle 4.37345 ( 2229) covalent geometry : bond 0.00348 ( 7633) covalent geometry : angle 0.52022 (10378) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.772 Fit side-chains REVERT: 2 75 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8222 (tmm) REVERT: 3 52 ARG cc_start: 0.8701 (ptt-90) cc_final: 0.8407 (ptt-90) REVERT: 4 45 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6581 (tpt90) REVERT: 5 45 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6951 (ptm160) REVERT: 5 52 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7175 (mtm180) REVERT: 6 45 ARG cc_start: 0.7906 (ttm-80) cc_final: 0.7702 (ttp-110) REVERT: 6 74 PHE cc_start: 0.8427 (m-80) cc_final: 0.8049 (m-80) REVERT: a 50 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6514 (ttm170) REVERT: a 76 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7430 (mp10) REVERT: a 80 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.7994 (t) REVERT: d 1 MET cc_start: 0.7614 (tpp) cc_final: 0.7253 (tpt) REVERT: d 5 ILE cc_start: 0.7800 (mm) cc_final: 0.7531 (mp) REVERT: d 27 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.6491 (ttm-80) outliers start: 25 outliers final: 6 residues processed: 116 average time/residue: 1.0925 time to fit residues: 134.8584 Evaluate side-chains 112 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 52 ARG Chi-restraints excluded: chain 6 residue 54 PHE Chi-restraints excluded: chain 6 residue 72 LEU Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 16 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 4 optimal weight: 0.0170 chunk 41 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN a 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112638 restraints weight = 8725.880| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.56 r_work: 0.3285 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7633 Z= 0.149 Angle : 0.519 6.558 10378 Z= 0.274 Chirality : 0.039 0.175 1235 Planarity : 0.004 0.042 1309 Dihedral : 5.498 71.629 1110 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.31 % Allowed : 13.98 % Favored : 82.71 % 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: 3.60 (0.25), residues: 1019 helix: 2.84 (0.17), residues: 842 sheet: -2.18 (1.38), residues: 9 loop : 0.16 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP b 48 HIS 0.003 0.001 HIS a 146 PHE 0.019 0.002 PHE 1 69 TYR 0.022 0.001 TYR a 145 ARG 0.006 0.001 ARG 1 52 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 746) hydrogen bonds : angle 4.32275 ( 2229) covalent geometry : bond 0.00321 ( 7633) covalent geometry : angle 0.51919 (10378) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.787 Fit side-chains REVERT: 2 21 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7975 (mmm) REVERT: 2 75 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8127 (tmm) REVERT: 3 52 ARG cc_start: 0.8710 (ptt-90) cc_final: 0.8435 (ptt-90) REVERT: 4 45 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6595 (tpt90) REVERT: 5 45 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6942 (ptm160) REVERT: 5 52 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7163 (mtm180) REVERT: 6 74 PHE cc_start: 0.8401 (m-80) cc_final: 0.8055 (m-80) REVERT: a 50 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6489 (ttm170) REVERT: a 76 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7440 (mp10) REVERT: a 80 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.7930 (t) REVERT: d 1 MET cc_start: 0.7634 (tpp) cc_final: 0.7298 (tpt) REVERT: d 5 ILE cc_start: 0.7760 (mm) cc_final: 0.7493 (mp) REVERT: d 27 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6508 (ttm-80) outliers start: 23 outliers final: 7 residues processed: 118 average time/residue: 1.1095 time to fit residues: 139.0600 Evaluate side-chains 120 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 52 ARG Chi-restraints excluded: chain 8 residue 6 ASN Chi-restraints excluded: chain 8 residue 85 LEU Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 64 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** a 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.133750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111235 restraints weight = 8842.193| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.57 r_work: 0.3262 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7633 Z= 0.171 Angle : 0.540 7.628 10378 Z= 0.286 Chirality : 0.040 0.168 1235 Planarity : 0.004 0.053 1309 Dihedral : 5.584 72.988 1110 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.75 % Allowed : 14.27 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.25), residues: 1019 helix: 2.77 (0.17), residues: 842 sheet: -2.06 (1.43), residues: 9 loop : 0.11 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP b 48 HIS 0.006 0.001 HIS a 16 PHE 0.018 0.002 PHE 1 69 TYR 0.023 0.001 TYR a 145 ARG 0.011 0.001 ARG 1 52 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 746) hydrogen bonds : angle 4.37581 ( 2229) covalent geometry : bond 0.00385 ( 7633) covalent geometry : angle 0.53969 (10378) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.756 Fit side-chains REVERT: 2 21 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8069 (mmm) REVERT: 2 75 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8114 (tmm) REVERT: 4 45 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6849 (tmt-80) REVERT: 5 45 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6939 (ptm160) REVERT: 5 75 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7893 (ttp) REVERT: 6 74 PHE cc_start: 0.8333 (m-80) cc_final: 0.8096 (m-80) REVERT: 6 75 MET cc_start: 0.8023 (ttp) cc_final: 0.7622 (ttt) REVERT: a 50 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6544 (ttm170) REVERT: a 76 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: a 80 SER cc_start: 0.8280 (OUTLIER) cc_final: 0.7999 (t) REVERT: d 1 MET cc_start: 0.7680 (tpp) cc_final: 0.7349 (tpt) REVERT: d 5 ILE cc_start: 0.7765 (mm) cc_final: 0.7500 (mp) REVERT: d 27 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.6506 (ttm-80) outliers start: 26 outliers final: 7 residues processed: 116 average time/residue: 1.1429 time to fit residues: 140.5548 Evaluate side-chains 115 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 75 MET Chi-restraints excluded: chain 6 residue 54 PHE Chi-restraints excluded: chain 8 residue 6 ASN Chi-restraints excluded: chain 8 residue 85 LEU Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 12 optimal weight: 0.8980 chunk 101 optimal weight: 0.0070 chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 95 optimal weight: 0.0770 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN a 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.137370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.114889 restraints weight = 8887.193| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.58 r_work: 0.3314 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7633 Z= 0.135 Angle : 0.511 6.562 10378 Z= 0.269 Chirality : 0.039 0.147 1235 Planarity : 0.004 0.042 1309 Dihedral : 5.397 71.712 1110 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.03 % Allowed : 14.99 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.26), residues: 1019 helix: 2.96 (0.17), residues: 842 sheet: -2.01 (1.42), residues: 9 loop : 0.14 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP b 48 HIS 0.005 0.001 HIS a 16 PHE 0.018 0.001 PHE a 194 TYR 0.021 0.001 TYR a 145 ARG 0.004 0.001 ARG 1 52 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 746) hydrogen bonds : angle 4.26635 ( 2229) covalent geometry : bond 0.00281 ( 7633) covalent geometry : angle 0.51057 (10378) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.678 Fit side-chains REVERT: 2 21 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7957 (mmm) REVERT: 2 75 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8054 (tmm) REVERT: 4 45 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.6861 (tmt170) REVERT: 5 45 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6852 (ptm160) REVERT: 5 75 MET cc_start: 0.8024 (ttp) cc_final: 0.7811 (ttp) REVERT: 6 75 MET cc_start: 0.7994 (ttp) cc_final: 0.7563 (ttt) REVERT: a 50 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6495 (ttm170) REVERT: a 76 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7471 (mp10) REVERT: a 80 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.7979 (t) REVERT: d 1 MET cc_start: 0.7648 (tpp) cc_final: 0.7326 (tpt) REVERT: d 5 ILE cc_start: 0.7756 (mm) cc_final: 0.7498 (mp) outliers start: 21 outliers final: 5 residues processed: 123 average time/residue: 1.0645 time to fit residues: 139.2724 Evaluate side-chains 120 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** a 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.135251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.112763 restraints weight = 8909.950| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.57 r_work: 0.3282 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7633 Z= 0.166 Angle : 0.553 10.408 10378 Z= 0.288 Chirality : 0.040 0.153 1235 Planarity : 0.004 0.046 1309 Dihedral : 5.492 72.159 1110 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.88 % Allowed : 15.85 % Favored : 81.27 % 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: 3.63 (0.25), residues: 1019 helix: 2.87 (0.17), residues: 842 sheet: -2.13 (1.43), residues: 9 loop : 0.11 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP b 48 HIS 0.006 0.001 HIS a 16 PHE 0.019 0.002 PHE a 194 TYR 0.022 0.001 TYR a 145 ARG 0.006 0.001 ARG 1 52 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 746) hydrogen bonds : angle 4.33251 ( 2229) covalent geometry : bond 0.00369 ( 7633) covalent geometry : angle 0.55316 (10378) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.787 Fit side-chains REVERT: 2 21 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8025 (mmm) REVERT: 2 75 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8170 (tmm) REVERT: 4 45 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6826 (tmt-80) REVERT: 5 45 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6878 (ptm160) REVERT: 6 75 MET cc_start: 0.8043 (ttp) cc_final: 0.7651 (ttt) REVERT: a 47 PHE cc_start: 0.6712 (m-10) cc_final: 0.6488 (m-10) REVERT: a 50 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6652 (ttm170) REVERT: a 76 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: a 80 SER cc_start: 0.8269 (OUTLIER) cc_final: 0.7945 (t) REVERT: d 1 MET cc_start: 0.7674 (tpp) cc_final: 0.7349 (tpt) REVERT: d 5 ILE cc_start: 0.7770 (mm) cc_final: 0.7506 (mp) outliers start: 20 outliers final: 6 residues processed: 116 average time/residue: 1.1042 time to fit residues: 136.4902 Evaluate side-chains 116 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 8 residue 6 ASN Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN a 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.135415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112909 restraints weight = 8786.165| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.56 r_work: 0.3285 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7633 Z= 0.163 Angle : 0.546 7.530 10378 Z= 0.287 Chirality : 0.040 0.144 1235 Planarity : 0.004 0.049 1309 Dihedral : 5.513 72.695 1110 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.31 % Allowed : 16.71 % Favored : 80.98 % 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: 3.61 (0.25), residues: 1019 helix: 2.85 (0.17), residues: 842 sheet: -2.13 (1.43), residues: 9 loop : 0.08 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP b 48 HIS 0.005 0.001 HIS a 16 PHE 0.031 0.002 PHE 6 74 TYR 0.022 0.001 TYR a 145 ARG 0.007 0.001 ARG 5 52 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 746) hydrogen bonds : angle 4.34670 ( 2229) covalent geometry : bond 0.00359 ( 7633) covalent geometry : angle 0.54644 (10378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4719.37 seconds wall clock time: 82 minutes 0.31 seconds (4920.31 seconds total)