Starting phenix.real_space_refine on Sat Dec 28 01:50:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g07_29648/12_2024/8g07_29648.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g07_29648/12_2024/8g07_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_29648/12_2024/8g07_29648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g07_29648/12_2024/8g07_29648.map" model { file = "/net/cci-nas-00/data/ceres_data/8g07_29648/12_2024/8g07_29648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g07_29648/12_2024/8g07_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-5532/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: 5.34, per 1000 atoms: 0.72 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: 2.12 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: 0.58 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: 2.36 Time building geometry restraints manager: 2.38 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.530 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.120 ------------------------------------------------------------------------------- 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= 0.538 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 *********************** 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 : 0.802 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: 1.0657 time to fit residues: 142.0019 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 : 0.726 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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= 0.219 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 *********************** 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 : 0.691 Fit side-chains REVERT: 4 45 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6659 (tpt90) REVERT: 7 58 PHE cc_start: 0.7940 (m-80) cc_final: 0.7723 (m-80) REVERT: a 73 MET cc_start: 0.7867 (mmt) cc_final: 0.7072 (mmt) REVERT: a 75 GLN cc_start: 0.7855 (mt0) cc_final: 0.7597 (mt0) REVERT: a 210 ILE cc_start: 0.7480 (mm) cc_final: 0.7258 (tp) outliers start: 13 outliers final: 6 residues processed: 116 average time/residue: 1.0909 time to fit residues: 134.8373 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 : 0.834 ------------------------------------------------------------------------------- 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 51 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1864 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= 0.240 Angle : 0.535 6.516 10378 Z= 0.285 Chirality : 0.040 0.149 1235 Planarity : 0.004 0.042 1309 Dihedral : 5.496 62.518 1110 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: 3.51 (0.26), residues: 1019 helix: 2.72 (0.17), residues: 844 sheet: -1.91 (1.49), residues: 9 loop : 0.40 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 48 HIS 0.003 0.001 HIS a 15 PHE 0.019 0.002 PHE a 194 TYR 0.024 0.001 TYR a 145 ARG 0.004 0.000 ARG 1 52 *********************** 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 : 0.790 Fit side-chains REVERT: 2 75 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7668 (tmm) REVERT: 4 45 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6526 (tpt90) REVERT: a 76 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: a 210 ILE cc_start: 0.7386 (mm) cc_final: 0.7051 (tp) REVERT: d 1 MET cc_start: 0.7630 (tpp) cc_final: 0.7429 (tpp) outliers start: 19 outliers final: 6 residues processed: 119 average time/residue: 1.1986 time to fit residues: 151.5271 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 : 0.736 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 215 ASN a 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2048 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= 0.244 Angle : 0.542 7.661 10378 Z= 0.286 Chirality : 0.040 0.160 1235 Planarity : 0.004 0.041 1309 Dihedral : 5.518 65.364 1110 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: 3.54 (0.26), residues: 1019 helix: 2.75 (0.17), residues: 843 sheet: -2.00 (1.45), residues: 9 loop : 0.35 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 48 HIS 0.003 0.001 HIS a 146 PHE 0.018 0.002 PHE 6 74 TYR 0.023 0.001 TYR a 145 ARG 0.008 0.001 ARG 1 52 *********************** 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 128 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.746 Fit side-chains REVERT: 2 21 MET cc_start: 0.7575 (mmm) cc_final: 0.7286 (mmm) REVERT: 2 75 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7750 (tmm) REVERT: 4 45 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6517 (tpt90) REVERT: 5 45 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6564 (ptm160) REVERT: 5 52 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6549 (mtm180) REVERT: a 76 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: d 27 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.6102 (ttm-80) outliers start: 26 outliers final: 6 residues processed: 117 average time/residue: 1.0319 time to fit residues: 129.2970 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 : 0.826 ------------------------------------------------------------------------------- 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 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 215 ASN 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 82 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 0.0470 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2192 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= 0.213 Angle : 0.521 6.537 10378 Z= 0.276 Chirality : 0.040 0.171 1235 Planarity : 0.004 0.041 1309 Dihedral : 5.469 67.243 1110 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.60 % Allowed : 13.26 % Favored : 83.14 % 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 (0.26), residues: 1019 helix: 2.83 (0.17), residues: 842 sheet: -2.15 (1.38), residues: 9 loop : 0.25 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 48 HIS 0.003 0.001 HIS a 146 PHE 0.019 0.001 PHE 1 69 TYR 0.023 0.001 TYR a 145 ARG 0.006 0.001 ARG 1 52 *********************** 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 : 0.794 Fit side-chains REVERT: 2 21 MET cc_start: 0.7543 (mmm) cc_final: 0.7244 (mmm) REVERT: 2 75 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7648 (tmm) REVERT: 3 52 ARG cc_start: 0.8707 (ptt-90) cc_final: 0.8451 (ptt-90) REVERT: 4 45 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6527 (tpt90) REVERT: 5 45 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6618 (ptm160) REVERT: 5 52 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6526 (mtm180) REVERT: 6 45 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.7051 (ttp-110) REVERT: a 50 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.6092 (ttm170) REVERT: a 76 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7279 (mp10) REVERT: a 80 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.8031 (t) REVERT: d 27 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6429 (ttm-80) outliers start: 25 outliers final: 5 residues processed: 113 average time/residue: 1.1970 time to fit residues: 143.5716 Evaluate side-chains 112 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 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 a residue 215 ASN 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 33 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2267 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= 0.249 Angle : 0.534 6.556 10378 Z= 0.282 Chirality : 0.040 0.153 1235 Planarity : 0.004 0.042 1309 Dihedral : 5.523 69.434 1110 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.46 % Allowed : 14.12 % Favored : 82.42 % 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: 3.56 (0.26), residues: 1019 helix: 2.80 (0.17), residues: 842 sheet: -2.20 (1.38), residues: 9 loop : 0.21 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 48 HIS 0.003 0.001 HIS a 146 PHE 0.021 0.002 PHE 1 69 TYR 0.023 0.001 TYR a 145 ARG 0.004 0.000 ARG 1 52 *********************** 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 126 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.766 Fit side-chains REVERT: 2 21 MET cc_start: 0.7514 (mmm) cc_final: 0.7045 (tpt) REVERT: 2 75 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7638 (tmm) REVERT: 4 45 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6544 (tpt90) REVERT: 5 45 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6623 (ptm160) REVERT: 5 52 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6546 (mtm180) REVERT: a 50 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6081 (ttm170) REVERT: a 76 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7344 (mp10) REVERT: a 80 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.8017 (t) REVERT: d 27 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6508 (ttm-80) outliers start: 24 outliers final: 7 residues processed: 113 average time/residue: 1.1562 time to fit residues: 138.8501 Evaluate side-chains 110 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 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 198 ILE Chi-restraints excluded: chain a residue 215 ASN 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 96 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2332 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= 0.239 Angle : 0.536 6.960 10378 Z= 0.282 Chirality : 0.040 0.179 1235 Planarity : 0.004 0.042 1309 Dihedral : 5.534 71.123 1110 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.60 % Allowed : 13.98 % Favored : 82.42 % 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: 3.54 (0.26), residues: 1019 helix: 2.79 (0.17), residues: 842 sheet: -2.32 (1.35), residues: 9 loop : 0.16 (0.49), 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 0.020 0.002 PHE 1 69 TYR 0.023 0.001 TYR a 145 ARG 0.006 0.000 ARG 1 52 *********************** 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 122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.776 Fit side-chains REVERT: 2 21 MET cc_start: 0.7519 (mmm) cc_final: 0.7054 (tpt) REVERT: 2 75 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7611 (tmm) REVERT: 4 45 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6497 (tpt90) REVERT: 5 45 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6645 (ptm160) REVERT: 5 52 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6533 (mtm180) REVERT: a 50 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6136 (ttm170) REVERT: a 76 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7321 (mp10) REVERT: a 80 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.8057 (t) REVERT: d 27 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.6489 (ttm-80) outliers start: 25 outliers final: 7 residues processed: 108 average time/residue: 1.1804 time to fit residues: 135.4750 Evaluate side-chains 111 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 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 198 ILE Chi-restraints excluded: chain a residue 215 ASN 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 39 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2365 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= 0.252 Angle : 0.544 7.575 10378 Z= 0.287 Chirality : 0.040 0.166 1235 Planarity : 0.004 0.058 1309 Dihedral : 5.564 72.402 1110 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.31 % Allowed : 14.84 % Favored : 81.84 % 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 (0.26), residues: 1019 helix: 2.77 (0.17), residues: 842 sheet: -2.24 (1.36), residues: 9 loop : 0.14 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP b 48 HIS 0.002 0.001 HIS a 146 PHE 0.019 0.002 PHE 1 69 TYR 0.023 0.001 TYR a 145 ARG 0.012 0.001 ARG 1 52 *********************** 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 125 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.801 Fit side-chains REVERT: 2 21 MET cc_start: 0.7511 (mmm) cc_final: 0.7066 (tpt) REVERT: 2 75 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7629 (tmm) REVERT: 4 45 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6461 (tpt90) REVERT: 5 45 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6658 (ptm160) REVERT: 5 52 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6539 (mtm180) REVERT: 6 75 MET cc_start: 0.7450 (ttp) cc_final: 0.7234 (ttt) REVERT: a 50 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6148 (ttm170) REVERT: a 76 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7329 (mp10) REVERT: a 80 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.8106 (t) REVERT: d 27 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.6513 (ttm-80) outliers start: 23 outliers final: 10 residues processed: 113 average time/residue: 1.2002 time to fit residues: 144.5285 Evaluate side-chains 113 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 5 residue 52 ARG Chi-restraints excluded: chain 6 residue 72 LEU 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 a residue 215 ASN 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 86 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2431 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= 0.223 Angle : 0.534 7.048 10378 Z= 0.281 Chirality : 0.040 0.157 1235 Planarity : 0.004 0.057 1309 Dihedral : 5.532 72.789 1110 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.46 % Allowed : 14.84 % Favored : 81.70 % 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: 3.55 (0.26), residues: 1019 helix: 2.81 (0.17), residues: 842 sheet: -2.15 (1.39), residues: 9 loop : 0.11 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP b 48 HIS 0.003 0.001 HIS a 16 PHE 0.023 0.002 PHE 6 74 TYR 0.022 0.001 TYR a 145 ARG 0.013 0.001 ARG 1 52 *********************** 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 123 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.807 Fit side-chains REVERT: 2 21 MET cc_start: 0.7487 (mmm) cc_final: 0.7040 (tpt) REVERT: 2 75 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7610 (tmm) REVERT: 4 45 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6609 (tmt-80) REVERT: 5 45 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6561 (ptm160) REVERT: 5 52 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6521 (mtm180) REVERT: 6 75 MET cc_start: 0.7486 (ttp) cc_final: 0.7253 (ttt) REVERT: a 50 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.6107 (ttm170) REVERT: a 76 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: a 80 SER cc_start: 0.8345 (OUTLIER) cc_final: 0.8102 (t) REVERT: d 27 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.6480 (ttm-80) outliers start: 24 outliers final: 11 residues processed: 110 average time/residue: 1.1617 time to fit residues: 135.8352 Evaluate side-chains 115 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 5 residue 52 ARG Chi-restraints excluded: chain 5 residue 75 MET Chi-restraints excluded: chain 6 residue 72 LEU 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 a residue 215 ASN Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain d residue 27 ARG 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 46 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 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** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2417 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= 0.265 Angle : 0.553 7.999 10378 Z= 0.291 Chirality : 0.040 0.155 1235 Planarity : 0.004 0.042 1309 Dihedral : 5.594 73.472 1110 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.11 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: 3.46 (0.26), residues: 1019 helix: 2.75 (0.17), residues: 842 sheet: -2.16 (1.39), residues: 9 loop : 0.06 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP b 48 HIS 0.004 0.001 HIS a 16 PHE 0.019 0.002 PHE 1 69 TYR 0.022 0.001 TYR a 145 ARG 0.005 0.001 ARG 1 52 ********************** 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 118 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.742 Fit side-chains REVERT: 2 21 MET cc_start: 0.7516 (mmm) cc_final: 0.7072 (tpt) REVERT: 2 75 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7632 (tmm) REVERT: 4 45 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6641 (tmt-80) REVERT: 5 45 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6609 (ptm160) REVERT: 5 52 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6547 (mtm180) REVERT: 6 75 MET cc_start: 0.7491 (ttp) cc_final: 0.7223 (ttt) REVERT: a 50 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.6145 (ttm170) REVERT: a 76 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: d 27 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6535 (ttm-80) outliers start: 20 outliers final: 12 residues processed: 108 average time/residue: 1.1469 time to fit residues: 131.4396 Evaluate side-chains 115 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 5 residue 52 ARG Chi-restraints excluded: chain 5 residue 75 MET Chi-restraints excluded: chain 6 residue 72 LEU 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 a residue 215 ASN Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 12 optimal weight: 0.0870 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 71 optimal weight: 0.0870 chunk 4 optimal weight: 0.3980 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 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 = 0.3702 r_free = 0.3702 target = 0.136989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114645 restraints weight = 8671.095| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.55 r_work: 0.3311 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2551 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= 0.181 Angle : 0.522 6.557 10378 Z= 0.274 Chirality : 0.039 0.143 1235 Planarity : 0.004 0.047 1309 Dihedral : 5.419 72.474 1110 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.74 % Allowed : 16.14 % Favored : 81.12 % 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: 3.68 (0.26), residues: 1019 helix: 2.91 (0.17), residues: 842 sheet: -2.10 (1.39), residues: 9 loop : 0.10 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP b 48 HIS 0.003 0.001 HIS a 16 PHE 0.025 0.001 PHE 6 74 TYR 0.021 0.001 TYR a 145 ARG 0.005 0.001 ARG 1 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2691.50 seconds wall clock time: 49 minutes 14.08 seconds (2954.08 seconds total)