Starting phenix.real_space_refine on Wed Mar 12 05:28:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g07_29648/03_2025/8g07_29648.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g07_29648/03_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_29648/03_2025/8g07_29648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g07_29648/03_2025/8g07_29648.map" model { file = "/net/cci-nas-00/data/ceres_data/8g07_29648/03_2025/8g07_29648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g07_29648/03_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-5624/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: 5.53, per 1000 atoms: 0.74 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: 2.25 Conformation dependent library (CDL) restraints added in 1.2 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: 0.61 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: 2.55 Time building geometry restraints manager: 2.60 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: 2.670 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.770 Find NCS groups from input model: 0.290 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.560 ------------------------------------------------------------------------------- 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 : 0.715 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: 1.2343 time to fit residues: 164.6897 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 : 0.768 ------------------------------------------------------------------------------- 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: 0.0070 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: 0.0570 chunk 93 optimal weight: 0.9980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 6 ASN 7 46 GLN ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 46 GLN 9 50 GLN ** a 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.137062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114825 restraints weight = 8441.118| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.54 r_work: 0.3318 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7633 Z= 0.202 Angle : 0.552 6.388 10378 Z= 0.294 Chirality : 0.040 0.161 1235 Planarity : 0.004 0.039 1309 Dihedral : 5.478 57.241 1110 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.16 % Allowed : 9.65 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.26), residues: 1019 helix: 2.47 (0.17), residues: 845 sheet: -1.93 (1.48), residues: 9 loop : 0.37 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 48 HIS 0.004 0.001 HIS a 146 PHE 0.019 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 122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.878 Fit side-chains REVERT: 4 45 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.6791 (tpt90) REVERT: a 73 MET cc_start: 0.8370 (mmt) cc_final: 0.7781 (mmt) REVERT: a 208 TRP cc_start: 0.8073 (p-90) cc_final: 0.7867 (p-90) REVERT: a 210 ILE cc_start: 0.7338 (mm) cc_final: 0.7045 (tp) outliers start: 15 outliers final: 5 residues processed: 116 average time/residue: 1.5808 time to fit residues: 195.5436 Evaluate side-chains 99 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 a residue 198 ILE Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain d residue 8 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 81 optimal weight: 0.0470 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 82 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 50 GLN a 63 GLN a 215 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.136338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113847 restraints weight = 8743.078| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.58 r_work: 0.3298 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1887 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= 0.203 Angle : 0.521 6.516 10378 Z= 0.275 Chirality : 0.040 0.139 1235 Planarity : 0.004 0.041 1309 Dihedral : 5.389 60.181 1110 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.59 % Allowed : 11.96 % Favored : 85.45 % 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: 3.70 (0.26), residues: 1019 helix: 2.88 (0.17), residues: 843 sheet: -1.94 (1.48), residues: 9 loop : 0.34 (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 0.019 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 129 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.699 Fit side-chains REVERT: 1 21 MET cc_start: 0.8026 (mmm) cc_final: 0.7745 (mmp) REVERT: 2 75 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8141 (tmm) REVERT: 4 21 MET cc_start: 0.8524 (mmm) cc_final: 0.8320 (mmm) REVERT: 4 45 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.6690 (tpt90) REVERT: 8 53 LEU cc_start: 0.8599 (mt) cc_final: 0.8386 (mp) REVERT: a 73 MET cc_start: 0.8436 (mmt) cc_final: 0.7679 (mmt) REVERT: a 210 ILE cc_start: 0.7304 (mm) cc_final: 0.6983 (tp) REVERT: d 1 MET cc_start: 0.7496 (tpp) cc_final: 0.6992 (tpp) REVERT: d 5 ILE cc_start: 0.7829 (mm) cc_final: 0.7543 (mp) outliers start: 18 outliers final: 5 residues processed: 122 average time/residue: 1.4405 time to fit residues: 187.4280 Evaluate side-chains 107 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 a residue 58 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 11 optimal weight: 0.9990 chunk 79 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 a 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113514 restraints weight = 8712.002| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.56 r_work: 0.3299 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2057 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 : 0.527 7.677 10378 Z= 0.276 Chirality : 0.039 0.157 1235 Planarity : 0.004 0.041 1309 Dihedral : 5.399 62.764 1110 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.31 % Allowed : 12.10 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.26), residues: 1019 helix: 2.94 (0.17), residues: 843 sheet: -2.00 (1.45), residues: 9 loop : 0.32 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 48 HIS 0.003 0.001 HIS a 146 PHE 0.019 0.002 PHE a 194 TYR 0.023 0.001 TYR a 145 ARG 0.004 0.000 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 131 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.726 Fit side-chains REVERT: 2 75 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8224 (tmm) REVERT: 4 45 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6639 (tpt90) REVERT: 8 53 LEU cc_start: 0.8667 (mt) cc_final: 0.8463 (mp) REVERT: a 76 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7541 (mp10) REVERT: a 210 ILE cc_start: 0.7221 (mm) cc_final: 0.6848 (tp) REVERT: d 1 MET cc_start: 0.7502 (tpp) cc_final: 0.7030 (tpp) REVERT: d 5 ILE cc_start: 0.7872 (mm) cc_final: 0.7589 (mp) REVERT: d 27 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6149 (ttm-80) outliers start: 23 outliers final: 7 residues processed: 119 average time/residue: 0.9705 time to fit residues: 123.6445 Evaluate side-chains 110 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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 198 ILE 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: 5.9990 chunk 7 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 83 optimal weight: 0.0570 chunk 90 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 a 192 ASN a 215 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114392 restraints weight = 8629.320| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.55 r_work: 0.3308 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2261 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= 0.193 Angle : 0.511 6.548 10378 Z= 0.268 Chirality : 0.039 0.169 1235 Planarity : 0.004 0.041 1309 Dihedral : 5.345 65.156 1110 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.60 % Allowed : 13.54 % Favored : 82.85 % 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: 3.89 (0.26), residues: 1019 helix: 3.03 (0.17), residues: 843 sheet: -2.19 (1.37), residues: 9 loop : 0.28 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 48 HIS 0.003 0.001 HIS a 146 PHE 0.018 0.001 PHE a 194 TYR 0.022 0.001 TYR a 145 ARG 0.008 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 134 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.751 Fit side-chains REVERT: 2 75 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8154 (tmm) REVERT: 3 52 ARG cc_start: 0.8724 (ptt-90) cc_final: 0.8456 (ptt-90) REVERT: 4 45 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6635 (tpt90) REVERT: 5 45 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6924 (ptm160) REVERT: 6 69 PHE cc_start: 0.7750 (m-10) cc_final: 0.7332 (m-10) REVERT: a 76 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: a 80 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7898 (t) REVERT: d 1 MET cc_start: 0.7526 (tpp) cc_final: 0.7177 (tpt) REVERT: d 5 ILE cc_start: 0.7851 (mm) cc_final: 0.7588 (mp) REVERT: d 27 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6495 (ttm-80) outliers start: 25 outliers final: 5 residues processed: 117 average time/residue: 1.0635 time to fit residues: 133.2697 Evaluate side-chains 113 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 70 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 82 optimal weight: 0.0670 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 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 = 0.3677 r_free = 0.3677 target = 0.135070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112666 restraints weight = 8741.420| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.56 r_work: 0.3285 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2303 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= 0.233 Angle : 0.529 6.583 10378 Z= 0.278 Chirality : 0.040 0.154 1235 Planarity : 0.004 0.042 1309 Dihedral : 5.421 67.274 1110 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.60 % Allowed : 14.41 % 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: 3.79 (0.26), residues: 1019 helix: 2.96 (0.17), residues: 843 sheet: -2.41 (1.32), residues: 9 loop : 0.28 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 48 HIS 0.002 0.001 HIS a 146 PHE 0.020 0.002 PHE 1 69 TYR 0.022 0.001 TYR a 145 ARG 0.010 0.001 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 133 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.756 Fit side-chains REVERT: 2 75 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8219 (tmm) REVERT: 3 52 ARG cc_start: 0.8715 (ptt-90) cc_final: 0.8411 (ptt-90) REVERT: 4 45 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.6827 (tmt-80) REVERT: 5 45 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6916 (ptm160) REVERT: 5 52 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7128 (mtm180) REVERT: 6 75 MET cc_start: 0.7934 (ttp) cc_final: 0.7541 (ttt) REVERT: a 50 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6512 (ttm170) REVERT: a 76 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7626 (mp10) REVERT: a 80 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8026 (t) REVERT: d 1 MET cc_start: 0.7552 (tpp) cc_final: 0.7182 (tpt) REVERT: d 5 ILE cc_start: 0.7826 (mm) cc_final: 0.7556 (mp) outliers start: 25 outliers final: 6 residues processed: 116 average time/residue: 1.0786 time to fit residues: 133.1364 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 : 0.702 ------------------------------------------------------------------------------- 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 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 b residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 4 optimal weight: 0.0270 chunk 41 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 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 = 0.3681 r_free = 0.3681 target = 0.135220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112902 restraints weight = 8756.230| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.56 r_work: 0.3295 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2405 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= 0.219 Angle : 0.532 9.252 10378 Z= 0.278 Chirality : 0.040 0.174 1235 Planarity : 0.004 0.042 1309 Dihedral : 5.424 69.859 1110 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.31 % Allowed : 14.99 % 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: 3.78 (0.26), residues: 1019 helix: 2.96 (0.17), residues: 842 sheet: -2.22 (1.35), residues: 9 loop : 0.23 (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 0.019 0.002 PHE 1 69 TYR 0.022 0.001 TYR a 145 ARG 0.011 0.001 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 131 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.734 Fit side-chains REVERT: 2 75 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8124 (tmm) REVERT: 3 52 ARG cc_start: 0.8720 (ptt-90) cc_final: 0.8420 (ptt-90) REVERT: 4 45 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.6906 (tmt-80) REVERT: 5 45 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6872 (ptm160) REVERT: 5 52 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7111 (mtm180) REVERT: a 50 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6494 (ttm170) REVERT: a 76 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7659 (mp10) REVERT: a 80 SER cc_start: 0.8246 (OUTLIER) cc_final: 0.7937 (t) REVERT: d 1 MET cc_start: 0.7601 (tpp) cc_final: 0.7266 (tpt) REVERT: d 5 ILE cc_start: 0.7869 (mm) cc_final: 0.7612 (mp) outliers start: 23 outliers final: 5 residues processed: 117 average time/residue: 1.2124 time to fit residues: 150.6645 Evaluate side-chains 112 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 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 b residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 64 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 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 = 0.3667 r_free = 0.3667 target = 0.133783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.111310 restraints weight = 8862.256| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.57 r_work: 0.3268 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7633 Z= 0.267 Angle : 0.560 8.105 10378 Z= 0.293 Chirality : 0.041 0.168 1235 Planarity : 0.004 0.053 1309 Dihedral : 5.561 72.801 1110 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.03 % Allowed : 15.85 % 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: 3.59 (0.26), residues: 1019 helix: 2.83 (0.17), residues: 842 sheet: -2.13 (1.40), residues: 9 loop : 0.14 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP b 48 HIS 0.008 0.001 HIS a 16 PHE 0.019 0.002 PHE 1 69 TYR 0.022 0.001 TYR a 145 ARG 0.011 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 131 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.776 Fit side-chains REVERT: 2 75 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8270 (tmm) REVERT: 4 45 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.6815 (tmt-80) REVERT: 5 45 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6941 (ptm160) REVERT: 5 52 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7196 (mtm180) REVERT: 6 75 MET cc_start: 0.7999 (ttp) cc_final: 0.7689 (ttt) REVERT: a 50 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6537 (ttm170) REVERT: a 76 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: a 80 SER cc_start: 0.8227 (OUTLIER) cc_final: 0.7894 (t) REVERT: d 1 MET cc_start: 0.7634 (tpp) cc_final: 0.7297 (tpt) REVERT: d 5 ILE cc_start: 0.7767 (mm) cc_final: 0.7500 (mp) outliers start: 21 outliers final: 7 residues processed: 119 average time/residue: 1.0946 time to fit residues: 138.5475 Evaluate side-chains 118 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 198 ILE Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 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** 7 46 GLN 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 = 0.3683 r_free = 0.3683 target = 0.135283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112836 restraints weight = 8901.206| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.57 r_work: 0.3287 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2490 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 : 0.548 9.626 10378 Z= 0.286 Chirality : 0.040 0.173 1235 Planarity : 0.004 0.055 1309 Dihedral : 5.519 73.552 1110 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.17 % Allowed : 15.99 % Favored : 80.84 % 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: 3.62 (0.25), residues: 1019 helix: 2.86 (0.17), residues: 842 sheet: -2.08 (1.41), residues: 9 loop : 0.14 (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 0.029 0.002 PHE 6 74 TYR 0.022 0.001 TYR a 145 ARG 0.012 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 129 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.840 Fit side-chains REVERT: 2 75 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8180 (tmm) REVERT: 4 45 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.6838 (tmt-80) REVERT: 5 45 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6857 (ptm160) REVERT: 5 52 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7169 (mtm180) REVERT: 6 75 MET cc_start: 0.8022 (ttp) cc_final: 0.7696 (ttt) REVERT: a 50 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6513 (ttm170) REVERT: a 76 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7665 (mp10) REVERT: a 80 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7975 (t) REVERT: d 1 MET cc_start: 0.7623 (tpp) cc_final: 0.7288 (tpt) REVERT: d 5 ILE cc_start: 0.7765 (mm) cc_final: 0.7496 (mp) outliers start: 22 outliers final: 7 residues processed: 116 average time/residue: 1.1711 time to fit residues: 144.2565 Evaluate side-chains 115 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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 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 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: 4.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 72 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.0970 chunk 86 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 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 = 0.3689 r_free = 0.3689 target = 0.135903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113378 restraints weight = 8862.439| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.57 r_work: 0.3296 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2532 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= 0.215 Angle : 0.538 6.899 10378 Z= 0.283 Chirality : 0.040 0.149 1235 Planarity : 0.004 0.047 1309 Dihedral : 5.494 73.931 1110 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.88 % Allowed : 15.99 % 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: 3.65 (0.25), residues: 1019 helix: 2.87 (0.17), residues: 842 sheet: -2.06 (1.42), residues: 9 loop : 0.18 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP b 48 HIS 0.007 0.001 HIS a 16 PHE 0.018 0.001 PHE a 194 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 122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.726 Fit side-chains REVERT: 2 75 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8183 (tmm) REVERT: 4 45 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6817 (tmt-80) REVERT: 5 45 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6899 (ptm160) REVERT: 5 52 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7166 (mtm180) REVERT: 6 75 MET cc_start: 0.7905 (ttp) cc_final: 0.7594 (ttt) REVERT: a 50 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6576 (ttm170) REVERT: a 73 MET cc_start: 0.8059 (tpp) cc_final: 0.7700 (mmp) REVERT: a 76 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: a 80 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.7969 (t) REVERT: d 1 MET cc_start: 0.7635 (tpp) cc_final: 0.7300 (tpt) REVERT: d 5 ILE cc_start: 0.7743 (mm) cc_final: 0.7476 (mp) outliers start: 20 outliers final: 8 residues processed: 112 average time/residue: 1.1593 time to fit residues: 137.5787 Evaluate side-chains 117 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 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 a residue 162 VAL Chi-restraints excluded: chain a residue 198 ILE 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: 0.7980 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 0.0040 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 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 = 0.3691 r_free = 0.3691 target = 0.136120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.113795 restraints weight = 8760.989| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.54 r_work: 0.3302 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2568 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= 0.221 Angle : 0.546 9.807 10378 Z= 0.285 Chirality : 0.040 0.143 1235 Planarity : 0.004 0.050 1309 Dihedral : 5.491 73.559 1110 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.74 % Allowed : 16.28 % 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: 3.65 (0.25), residues: 1019 helix: 2.87 (0.17), residues: 842 sheet: -2.17 (1.41), residues: 9 loop : 0.19 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP b 48 HIS 0.007 0.001 HIS a 16 PHE 0.027 0.002 PHE 6 74 TYR 0.022 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: 5105.91 seconds wall clock time: 90 minutes 28.46 seconds (5428.46 seconds total)