Starting phenix.real_space_refine on Fri Aug 22 18:39:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j57_35982/08_2025/8j57_35982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j57_35982/08_2025/8j57_35982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j57_35982/08_2025/8j57_35982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j57_35982/08_2025/8j57_35982.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j57_35982/08_2025/8j57_35982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j57_35982/08_2025/8j57_35982.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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: 5 Type Number sf(0) Gaussians Br 7 7.06 5 S 24 5.16 5 C 4689 2.51 5 N 1100 2.21 5 O 1187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7007 Number of models: 1 Model: "" Number of chains: 17 Chain: "1" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "2" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "3" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "4" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "5" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "6" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "7" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "8" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "9" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 550 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "a" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "1" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.14, per 1000 atoms: 0.31 Number of scatterers: 7007 At special positions: 0 Unit cell: (74.46, 97.82, 78.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 7 34.99 S 24 16.00 O 1187 8.00 N 1100 7.00 C 4689 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: 0.68 Conformation dependent library (CDL) restraints added in 392.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 89.5% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain '1' and resid 2 through 42 removed outlier: 3.704A pdb=" N ALA 1 34 " --> pdb=" O VAL 1 30 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 77 removed outlier: 3.674A pdb=" N PHE 1 50 " --> pdb=" O GLN 1 46 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR 1 51 " --> pdb=" O GLY 1 47 " (cutoff:3.500A) Proline residue: 1 52 - end of helix removed outlier: 3.553A pdb=" N ALA 1 63 " --> pdb=" O LEU 1 59 " (cutoff:3.500A) Processing helix chain '2' and resid 3 through 42 removed outlier: 3.799A pdb=" N ALA 2 34 " --> pdb=" O VAL 2 30 " (cutoff:3.500A) Processing helix chain '2' and resid 45 through 77 removed outlier: 4.328A pdb=" N THR 2 51 " --> pdb=" O GLY 2 47 " (cutoff:3.500A) Proline residue: 2 52 - end of helix Processing helix chain '3' and resid 3 through 42 removed outlier: 3.715A pdb=" N ALA 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) Processing helix chain '3' and resid 45 through 77 removed outlier: 4.135A pdb=" N THR 3 51 " --> pdb=" O GLY 3 47 " (cutoff:3.500A) Proline residue: 3 52 - end of helix removed outlier: 3.934A pdb=" N ALA 3 63 " --> pdb=" O LEU 3 59 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR 3 64 " --> pdb=" O VAL 3 60 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN 3 67 " --> pdb=" O ALA 3 63 " (cutoff:3.500A) Processing helix chain '4' and resid 3 through 42 removed outlier: 3.659A pdb=" N ALA 4 34 " --> pdb=" O VAL 4 30 " (cutoff:3.500A) Processing helix chain '4' and resid 45 through 77 removed outlier: 4.400A pdb=" N THR 4 51 " --> pdb=" O GLY 4 47 " (cutoff:3.500A) Proline residue: 4 52 - end of helix Processing helix chain '5' and resid 3 through 42 removed outlier: 3.833A pdb=" N ALA 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) Processing helix chain '5' and resid 45 through 77 removed outlier: 4.721A pdb=" N THR 5 51 " --> pdb=" O GLY 5 47 " (cutoff:3.500A) Proline residue: 5 52 - end of helix removed outlier: 3.508A pdb=" N ALA 5 63 " --> pdb=" O LEU 5 59 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 42 removed outlier: 3.659A pdb=" N ALA 6 34 " --> pdb=" O VAL 6 30 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 77 removed outlier: 3.507A pdb=" N PHE 6 50 " --> pdb=" O GLN 6 46 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR 6 51 " --> pdb=" O GLY 6 47 " (cutoff:3.500A) Proline residue: 6 52 - end of helix Processing helix chain '7' and resid 3 through 42 removed outlier: 3.679A pdb=" N ALA 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '7' and resid 45 through 77 removed outlier: 3.775A pdb=" N PHE 7 50 " --> pdb=" O GLN 7 46 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N THR 7 51 " --> pdb=" O GLY 7 47 " (cutoff:3.500A) Proline residue: 7 52 - end of helix Processing helix chain '8' and resid 3 through 42 removed outlier: 3.754A pdb=" N ALA 8 34 " --> pdb=" O VAL 8 30 " (cutoff:3.500A) Processing helix chain '8' and resid 45 through 77 removed outlier: 4.578A pdb=" N THR 8 51 " --> pdb=" O GLY 8 47 " (cutoff:3.500A) Proline residue: 8 52 - end of helix Processing helix chain '9' and resid 3 through 42 removed outlier: 3.817A pdb=" N ALA 9 34 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) Processing helix chain '9' and resid 45 through 77 removed outlier: 3.810A pdb=" N PHE 9 50 " --> pdb=" O GLN 9 46 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR 9 51 " --> pdb=" O GLY 9 47 " (cutoff:3.500A) Proline residue: 9 52 - end of helix Processing helix chain 'a' and resid 27 through 51 removed outlier: 5.885A pdb=" N SER a 32 " --> pdb=" O ASP a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 79 Processing helix chain 'a' and resid 86 through 104 removed outlier: 3.699A pdb=" N LEU a 90 " --> pdb=" O PHE a 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 107 No H-bonds generated for 'chain 'a' and resid 105 through 107' Processing helix chain 'a' and resid 124 through 127 Processing helix chain 'a' and resid 128 through 152 Processing helix chain 'a' and resid 154 through 163 Processing helix chain 'a' and resid 165 through 167 No H-bonds generated for 'chain 'a' and resid 165 through 167' Processing helix chain 'a' and resid 168 through 202 Proline residue: a 180 - end of helix removed outlier: 3.585A pdb=" N LEU a 187 " --> pdb=" O LEU a 183 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA a 199 " --> pdb=" O GLY a 195 " (cutoff:3.500A) Processing helix chain 'a' and resid 205 through 244 removed outlier: 3.815A pdb=" N TRP a 210 " --> pdb=" O PRO a 206 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA a 211 " --> pdb=" O TYR a 207 " (cutoff:3.500A) Proline residue: a 212 - end of helix removed outlier: 3.835A pdb=" N PHE a 222 " --> pdb=" O ALA a 218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 17 through 19 Processing sheet with id=AA2, first strand: chain 'a' and resid 110 through 111 672 hydrogen bonds defined for protein. 2010 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: 1.38 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 2181 1.36 - 1.50: 1947 1.50 - 1.65: 2997 1.65 - 1.79: 0 1.79 - 1.94: 54 Bond restraints: 7179 Sorted by residual: bond pdb=" C ALA 3 40 " pdb=" N ARG 3 41 " ideal model delta sigma weight residual 1.335 1.241 0.094 1.36e-02 5.41e+03 4.76e+01 bond pdb=" C ARG 6 41 " pdb=" N GLN 6 42 " ideal model delta sigma weight residual 1.332 1.368 -0.036 7.50e-03 1.78e+04 2.32e+01 bond pdb=" N PRO a 108 " pdb=" CD PRO a 108 " ideal model delta sigma weight residual 1.473 1.407 0.066 1.40e-02 5.10e+03 2.22e+01 bond pdb=" CE1 HIS a 156 " pdb=" NE2 HIS a 156 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.69e+01 bond pdb=" C10 BQ1 4 600 " pdb=" C17 BQ1 4 600 " ideal model delta sigma weight residual 1.437 1.363 0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 7174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 7296 1.82 - 3.65: 2154 3.65 - 5.47: 327 5.47 - 7.29: 23 7.29 - 9.12: 1 Bond angle restraints: 9801 Sorted by residual: angle pdb=" CA GLY a 152 " pdb=" C GLY a 152 " pdb=" O GLY a 152 " ideal model delta sigma weight residual 122.23 118.20 4.03 6.90e-01 2.10e+00 3.41e+01 angle pdb=" CA ALA 3 40 " pdb=" C ALA 3 40 " pdb=" N ARG 3 41 " ideal model delta sigma weight residual 117.30 123.79 -6.49 1.16e+00 7.43e-01 3.13e+01 angle pdb=" C ILE 6 11 " pdb=" N GLY 6 12 " pdb=" CA GLY 6 12 " ideal model delta sigma weight residual 119.94 124.77 -4.83 1.11e+00 8.12e-01 1.90e+01 angle pdb=" C ILE 3 11 " pdb=" N GLY 3 12 " pdb=" CA GLY 3 12 " ideal model delta sigma weight residual 119.98 124.69 -4.71 1.11e+00 8.12e-01 1.80e+01 angle pdb=" C ILE 2 11 " pdb=" N GLY 2 12 " pdb=" CA GLY 2 12 " ideal model delta sigma weight residual 119.94 124.49 -4.55 1.11e+00 8.12e-01 1.68e+01 ... (remaining 9796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.20: 3516 13.20 - 26.39: 399 26.39 - 39.58: 111 39.58 - 52.78: 36 52.78 - 65.97: 16 Dihedral angle restraints: 4078 sinusoidal: 1525 harmonic: 2553 Sorted by residual: dihedral pdb=" CA THR a 27 " pdb=" C THR a 27 " pdb=" N ASP a 28 " pdb=" CA ASP a 28 " ideal model delta harmonic sigma weight residual 180.00 156.86 23.14 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP a 28 " pdb=" C ASP a 28 " pdb=" N THR a 29 " pdb=" CA THR a 29 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA 9 77 " pdb=" C ALA 9 77 " pdb=" N THR 9 78 " pdb=" CA THR 9 78 " ideal model delta harmonic sigma weight residual -180.00 -159.42 -20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 4075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 666 0.069 - 0.138: 360 0.138 - 0.208: 74 0.208 - 0.277: 31 0.277 - 0.346: 6 Chirality restraints: 1137 Sorted by residual: chirality pdb=" CA TYR a 143 " pdb=" N TYR a 143 " pdb=" C TYR a 143 " pdb=" CB TYR a 143 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA PHE 3 54 " pdb=" N PHE 3 54 " pdb=" C PHE 3 54 " pdb=" CB PHE 3 54 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA THR 9 51 " pdb=" N THR 9 51 " pdb=" C THR 9 51 " pdb=" CB THR 9 51 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1134 not shown) Planarity restraints: 1225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 216 " -0.099 2.00e-02 2.50e+03 4.82e-02 5.81e+01 pdb=" CG TRP a 216 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP a 216 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP a 216 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP a 216 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TRP a 216 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP a 216 " 0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 216 " -0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 216 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP a 216 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 103 " 0.085 2.00e-02 2.50e+03 4.36e-02 4.75e+01 pdb=" CG TRP a 103 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP a 103 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP a 103 " -0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP a 103 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TRP a 103 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP a 103 " -0.047 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 103 " 0.062 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 103 " -0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP a 103 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 111 " -0.057 2.00e-02 2.50e+03 4.45e-02 3.97e+01 pdb=" CG TYR a 111 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR a 111 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR a 111 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR a 111 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR a 111 " 0.048 2.00e-02 2.50e+03 pdb=" CZ TYR a 111 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR a 111 " -0.083 2.00e-02 2.50e+03 ... (remaining 1222 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 2458 2.90 - 3.40: 7521 3.40 - 3.90: 12613 3.90 - 4.40: 13664 4.40 - 4.90: 24568 Nonbonded interactions: 60824 Sorted by model distance: nonbonded pdb=" O ASP 2 2 " pdb=" N ALA 2 6 " model vdw 2.397 3.120 nonbonded pdb=" O ASP 7 2 " pdb=" N ALA 7 6 " model vdw 2.399 3.120 nonbonded pdb=" OE2 GLU 8 61 " pdb=" C26 BQ1 8 600 " model vdw 2.431 3.460 nonbonded pdb=" OE2 GLU 9 61 " pdb=" C26 BQ1 9 600 " model vdw 2.470 3.460 nonbonded pdb=" O ALA 6 40 " pdb=" NE2 GLN 7 42 " model vdw 2.471 3.120 ... (remaining 60819 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 2 through 80) selection = chain '2' selection = chain '3' selection = (chain '4' and resid 2 through 80) selection = (chain '5' and resid 2 through 80) selection = (chain '6' and resid 2 through 80) selection = (chain '7' and resid 2 through 80) selection = (chain '8' and resid 2 through 80) selection = (chain '9' and resid 2 through 80) } 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: 12.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.170 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 : 0.013 0.094 7179 Z= 0.758 Angle : 1.672 9.115 9801 Z= 1.159 Chirality : 0.087 0.346 1137 Planarity : 0.015 0.117 1225 Dihedral : 13.657 65.972 2472 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.26), residues: 921 helix: 0.00 (0.16), residues: 815 sheet: None (None), residues: 0 loop : -1.45 (0.64), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 5 48 TYR 0.083 0.012 TYR a 111 PHE 0.059 0.014 PHE a 192 TRP 0.099 0.026 TRP a 216 HIS 0.007 0.002 HIS a 15 Details of bonding type rmsd covalent geometry : bond 0.01277 ( 7179) covalent geometry : angle 1.67178 ( 9801) hydrogen bonds : bond 0.16210 ( 672) hydrogen bonds : angle 7.27343 ( 2010) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.309 Fit side-chains REVERT: a 71 MET cc_start: 0.8839 (mmt) cc_final: 0.8305 (mmt) REVERT: a 167 LEU cc_start: 0.8509 (mm) cc_final: 0.8294 (mm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.5581 time to fit residues: 58.4148 Evaluate side-chains 72 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 42 GLN a 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105749 restraints weight = 6208.386| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.62 r_work: 0.3128 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7179 Z= 0.170 Angle : 0.662 14.936 9801 Z= 0.332 Chirality : 0.044 0.141 1137 Planarity : 0.006 0.056 1225 Dihedral : 10.098 43.492 1160 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.41 % Allowed : 7.67 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.11 (0.28), residues: 921 helix: 2.54 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -0.74 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 7 48 TYR 0.027 0.002 TYR a 143 PHE 0.019 0.002 PHE a 192 TRP 0.010 0.002 TRP a 216 HIS 0.003 0.001 HIS a 144 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7179) covalent geometry : angle 0.66225 ( 9801) hydrogen bonds : bond 0.05213 ( 672) hydrogen bonds : angle 4.63491 ( 2010) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.242 Fit side-chains REVERT: 4 71 MET cc_start: 0.8468 (tmm) cc_final: 0.7913 (tmm) REVERT: 5 71 MET cc_start: 0.8680 (tmm) cc_final: 0.8351 (tmm) REVERT: a 71 MET cc_start: 0.8115 (mmt) cc_final: 0.7738 (mmt) REVERT: a 74 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: a 244 GLU cc_start: 0.7317 (tt0) cc_final: 0.6843 (tp30) outliers start: 9 outliers final: 2 residues processed: 93 average time/residue: 0.5884 time to fit residues: 57.7540 Evaluate side-chains 76 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 124 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 0.0070 chunk 11 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.107541 restraints weight = 6098.055| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.60 r_work: 0.3141 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7179 Z= 0.143 Angle : 0.608 14.757 9801 Z= 0.296 Chirality : 0.041 0.143 1137 Planarity : 0.005 0.047 1225 Dihedral : 9.464 42.882 1160 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.35 % Allowed : 9.39 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.85 (0.28), residues: 921 helix: 3.07 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -0.69 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 7 48 TYR 0.024 0.001 TYR a 143 PHE 0.019 0.002 PHE a 63 TRP 0.008 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7179) covalent geometry : angle 0.60760 ( 9801) hydrogen bonds : bond 0.04525 ( 672) hydrogen bonds : angle 4.33678 ( 2010) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.259 Fit side-chains REVERT: 2 50 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8078 (m-10) REVERT: 4 50 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8545 (m-10) REVERT: 4 71 MET cc_start: 0.8463 (tmm) cc_final: 0.8217 (tmm) REVERT: 5 71 MET cc_start: 0.8641 (tmm) cc_final: 0.8227 (tmm) REVERT: a 50 LYS cc_start: 0.7654 (mttm) cc_final: 0.7377 (mttp) REVERT: a 71 MET cc_start: 0.8073 (mmt) cc_final: 0.7754 (mmt) REVERT: a 74 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.6604 (mp10) REVERT: a 130 ASN cc_start: 0.7688 (m110) cc_final: 0.7375 (m-40) REVERT: a 244 GLU cc_start: 0.7272 (tt0) cc_final: 0.6829 (tp30) outliers start: 15 outliers final: 3 residues processed: 82 average time/residue: 0.6156 time to fit residues: 53.2301 Evaluate side-chains 75 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 50 PHE Chi-restraints excluded: chain 4 residue 50 PHE Chi-restraints excluded: chain 4 residue 78 THR Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 122 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106818 restraints weight = 6085.853| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.60 r_work: 0.3137 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7179 Z= 0.144 Angle : 0.604 14.463 9801 Z= 0.290 Chirality : 0.041 0.134 1137 Planarity : 0.006 0.107 1225 Dihedral : 9.337 42.639 1160 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.35 % Allowed : 9.55 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.98 (0.28), residues: 921 helix: 3.19 (0.18), residues: 777 sheet: None (None), residues: 0 loop : -0.84 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 1 48 TYR 0.022 0.001 TYR a 143 PHE 0.017 0.001 PHE a 140 TRP 0.007 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7179) covalent geometry : angle 0.60426 ( 9801) hydrogen bonds : bond 0.04435 ( 672) hydrogen bonds : angle 4.28343 ( 2010) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.273 Fit side-chains REVERT: 4 71 MET cc_start: 0.8584 (tmm) cc_final: 0.8105 (tmm) REVERT: 5 71 MET cc_start: 0.8636 (tmm) cc_final: 0.8294 (tmm) REVERT: a 48 ARG cc_start: 0.7899 (tmt170) cc_final: 0.6703 (ttm170) REVERT: a 50 LYS cc_start: 0.7714 (mttm) cc_final: 0.7457 (mttp) REVERT: a 71 MET cc_start: 0.8078 (mmt) cc_final: 0.7768 (mmt) REVERT: a 74 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7121 (mp10) REVERT: a 82 ARG cc_start: 0.7705 (ttt90) cc_final: 0.7379 (ttm-80) REVERT: a 130 ASN cc_start: 0.7699 (m110) cc_final: 0.7398 (m-40) REVERT: a 244 GLU cc_start: 0.7289 (tt0) cc_final: 0.6847 (tp30) outliers start: 15 outliers final: 4 residues processed: 80 average time/residue: 0.6430 time to fit residues: 54.1219 Evaluate side-chains 73 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 124 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 6 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 chunk 46 optimal weight: 0.0770 chunk 33 optimal weight: 0.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 42 GLN 9 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107705 restraints weight = 5779.080| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.49 r_work: 0.3054 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7179 Z= 0.133 Angle : 0.585 12.237 9801 Z= 0.279 Chirality : 0.041 0.126 1137 Planarity : 0.005 0.046 1225 Dihedral : 9.141 45.390 1160 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.66 % Allowed : 10.02 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.10 (0.28), residues: 921 helix: 3.30 (0.18), residues: 777 sheet: None (None), residues: 0 loop : -1.05 (0.46), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 6 48 TYR 0.020 0.001 TYR a 143 PHE 0.016 0.001 PHE a 140 TRP 0.007 0.001 TRP a 216 HIS 0.004 0.001 HIS a 144 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7179) covalent geometry : angle 0.58529 ( 9801) hydrogen bonds : bond 0.04230 ( 672) hydrogen bonds : angle 4.22038 ( 2010) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.242 Fit side-chains REVERT: 1 42 GLN cc_start: 0.7363 (mp10) cc_final: 0.6958 (mp10) REVERT: 1 71 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7384 (tmt) REVERT: 2 50 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7880 (m-10) REVERT: 5 71 MET cc_start: 0.8449 (tmm) cc_final: 0.8179 (tmm) REVERT: a 48 ARG cc_start: 0.7851 (tmt170) cc_final: 0.6770 (ttm170) REVERT: a 50 LYS cc_start: 0.7574 (mttm) cc_final: 0.7336 (mttp) REVERT: a 71 MET cc_start: 0.7755 (mmt) cc_final: 0.7463 (mmt) REVERT: a 74 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6825 (mp10) REVERT: a 82 ARG cc_start: 0.7737 (ttt90) cc_final: 0.7420 (ttm-80) REVERT: a 130 ASN cc_start: 0.7455 (m110) cc_final: 0.7167 (m-40) REVERT: a 145 THR cc_start: 0.8544 (t) cc_final: 0.8276 (p) REVERT: a 244 GLU cc_start: 0.7086 (tt0) cc_final: 0.6622 (tp30) outliers start: 17 outliers final: 3 residues processed: 81 average time/residue: 0.6260 time to fit residues: 53.2983 Evaluate side-chains 73 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 71 MET Chi-restraints excluded: chain 2 residue 50 PHE Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 124 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 73 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101266 restraints weight = 6048.078| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.59 r_work: 0.3058 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7179 Z= 0.229 Angle : 0.671 10.919 9801 Z= 0.326 Chirality : 0.044 0.158 1137 Planarity : 0.006 0.079 1225 Dihedral : 9.524 43.794 1160 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.03 % Allowed : 11.89 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.56 (0.29), residues: 921 helix: 2.69 (0.18), residues: 831 sheet: None (None), residues: 0 loop : -1.22 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 7 48 TYR 0.020 0.002 TYR a 143 PHE 0.020 0.002 PHE a 140 TRP 0.006 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 7179) covalent geometry : angle 0.67080 ( 9801) hydrogen bonds : bond 0.05177 ( 672) hydrogen bonds : angle 4.48684 ( 2010) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.288 Fit side-chains REVERT: 1 42 GLN cc_start: 0.7601 (mp10) cc_final: 0.7290 (mp10) REVERT: 4 71 MET cc_start: 0.8719 (tmm) cc_final: 0.8083 (tmm) REVERT: a 48 ARG cc_start: 0.7994 (tmt170) cc_final: 0.6816 (ttm170) REVERT: a 50 LYS cc_start: 0.7732 (mttm) cc_final: 0.7480 (mttp) REVERT: a 71 MET cc_start: 0.8104 (mmt) cc_final: 0.7778 (mmt) REVERT: a 74 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7121 (mp10) REVERT: a 82 ARG cc_start: 0.7803 (ttt90) cc_final: 0.7449 (ttm-80) REVERT: a 130 ASN cc_start: 0.7735 (m110) cc_final: 0.7438 (m-40) REVERT: a 244 GLU cc_start: 0.7433 (tt0) cc_final: 0.6963 (tp30) outliers start: 13 outliers final: 5 residues processed: 82 average time/residue: 0.7019 time to fit residues: 60.3656 Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 78 THR Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 124 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 21 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105722 restraints weight = 6008.937| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.60 r_work: 0.3122 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7179 Z= 0.149 Angle : 0.603 10.392 9801 Z= 0.291 Chirality : 0.041 0.130 1137 Planarity : 0.005 0.075 1225 Dihedral : 9.249 43.247 1160 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.88 % Allowed : 12.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.78 (0.28), residues: 921 helix: 3.09 (0.18), residues: 777 sheet: None (None), residues: 0 loop : -1.14 (0.46), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 1 48 TYR 0.020 0.001 TYR a 143 PHE 0.016 0.001 PHE a 140 TRP 0.008 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7179) covalent geometry : angle 0.60281 ( 9801) hydrogen bonds : bond 0.04484 ( 672) hydrogen bonds : angle 4.30661 ( 2010) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.251 Fit side-chains REVERT: 1 42 GLN cc_start: 0.7635 (mp10) cc_final: 0.7309 (mp10) REVERT: 2 50 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7947 (m-10) REVERT: 4 71 MET cc_start: 0.8673 (tmm) cc_final: 0.8399 (tmm) REVERT: 5 71 MET cc_start: 0.8627 (tmm) cc_final: 0.8299 (tmm) REVERT: a 48 ARG cc_start: 0.7956 (tmt170) cc_final: 0.6855 (ttm170) REVERT: a 50 LYS cc_start: 0.7776 (mttm) cc_final: 0.7539 (mttp) REVERT: a 71 MET cc_start: 0.8086 (mmt) cc_final: 0.7788 (mmt) REVERT: a 74 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7175 (mp10) REVERT: a 82 ARG cc_start: 0.7770 (ttt90) cc_final: 0.7411 (ttm-80) REVERT: a 145 THR cc_start: 0.8713 (t) cc_final: 0.8424 (p) REVERT: a 244 GLU cc_start: 0.7429 (tt0) cc_final: 0.6962 (tp30) outliers start: 12 outliers final: 3 residues processed: 80 average time/residue: 0.7093 time to fit residues: 59.4370 Evaluate side-chains 76 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 50 PHE Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.0010 chunk 63 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106721 restraints weight = 6103.230| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.62 r_work: 0.3142 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7179 Z= 0.140 Angle : 0.593 9.879 9801 Z= 0.284 Chirality : 0.041 0.140 1137 Planarity : 0.005 0.061 1225 Dihedral : 9.068 44.052 1160 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.41 % Allowed : 12.83 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.26 (0.27), residues: 921 helix: 3.44 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -0.61 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 1 48 TYR 0.020 0.001 TYR a 143 PHE 0.016 0.001 PHE a 140 TRP 0.007 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7179) covalent geometry : angle 0.59326 ( 9801) hydrogen bonds : bond 0.04301 ( 672) hydrogen bonds : angle 4.23396 ( 2010) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.241 Fit side-chains REVERT: 1 42 GLN cc_start: 0.7633 (mp10) cc_final: 0.7220 (mp10) REVERT: 2 50 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7993 (m-10) REVERT: 4 71 MET cc_start: 0.8654 (tmm) cc_final: 0.8368 (tmm) REVERT: 5 71 MET cc_start: 0.8585 (tmm) cc_final: 0.8266 (tmm) REVERT: a 50 LYS cc_start: 0.7796 (mttm) cc_final: 0.7358 (mttp) REVERT: a 71 MET cc_start: 0.8060 (mmt) cc_final: 0.7771 (mmt) REVERT: a 74 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7143 (mp10) REVERT: a 82 ARG cc_start: 0.7880 (ttt90) cc_final: 0.7490 (ttm-80) REVERT: a 145 THR cc_start: 0.8733 (t) cc_final: 0.8425 (p) REVERT: a 244 GLU cc_start: 0.7394 (tt0) cc_final: 0.6936 (tp30) outliers start: 9 outliers final: 3 residues processed: 77 average time/residue: 0.6563 time to fit residues: 53.1106 Evaluate side-chains 75 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 50 PHE Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 33 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.0030 chunk 32 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107291 restraints weight = 6005.597| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.60 r_work: 0.3142 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7179 Z= 0.142 Angle : 0.604 10.369 9801 Z= 0.288 Chirality : 0.041 0.136 1137 Planarity : 0.005 0.068 1225 Dihedral : 9.004 43.334 1160 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.10 % Allowed : 13.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.24 (0.27), residues: 921 helix: 3.45 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -0.72 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 1 48 TYR 0.020 0.001 TYR a 143 PHE 0.016 0.001 PHE a 140 TRP 0.007 0.001 TRP a 216 HIS 0.004 0.001 HIS a 144 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7179) covalent geometry : angle 0.60437 ( 9801) hydrogen bonds : bond 0.04318 ( 672) hydrogen bonds : angle 4.22044 ( 2010) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.262 Fit side-chains REVERT: 1 42 GLN cc_start: 0.7574 (mp10) cc_final: 0.7044 (mp10) REVERT: 1 46 GLN cc_start: 0.7875 (tt0) cc_final: 0.7157 (pt0) REVERT: 2 50 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8002 (m-10) REVERT: 4 71 MET cc_start: 0.8680 (tmm) cc_final: 0.8391 (tmm) REVERT: 5 71 MET cc_start: 0.8616 (tmm) cc_final: 0.8403 (tmm) REVERT: a 50 LYS cc_start: 0.7774 (mttm) cc_final: 0.7325 (mttp) REVERT: a 71 MET cc_start: 0.8048 (mmt) cc_final: 0.7759 (mmt) REVERT: a 74 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7168 (mp10) REVERT: a 82 ARG cc_start: 0.7902 (ttt90) cc_final: 0.7582 (ttm-80) REVERT: a 145 THR cc_start: 0.8750 (t) cc_final: 0.8439 (p) REVERT: a 244 GLU cc_start: 0.7401 (tt0) cc_final: 0.6926 (tp30) outliers start: 7 outliers final: 3 residues processed: 78 average time/residue: 0.6394 time to fit residues: 52.3690 Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 50 PHE Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.106101 restraints weight = 6018.771| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.60 r_work: 0.3126 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7179 Z= 0.152 Angle : 0.623 12.387 9801 Z= 0.296 Chirality : 0.041 0.135 1137 Planarity : 0.005 0.046 1225 Dihedral : 9.047 42.505 1160 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.94 % Allowed : 14.24 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.17 (0.27), residues: 921 helix: 3.38 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -0.63 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 1 48 TYR 0.020 0.001 TYR a 143 PHE 0.018 0.001 PHE 4 70 TRP 0.007 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 7179) covalent geometry : angle 0.62316 ( 9801) hydrogen bonds : bond 0.04452 ( 672) hydrogen bonds : angle 4.28177 ( 2010) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.317 Fit side-chains REVERT: 1 42 GLN cc_start: 0.7543 (mp10) cc_final: 0.7012 (mp10) REVERT: 1 46 GLN cc_start: 0.7934 (tt0) cc_final: 0.7169 (pt0) REVERT: 2 50 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: 9 46 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7715 (tm-30) REVERT: a 50 LYS cc_start: 0.7742 (mttm) cc_final: 0.7291 (mttp) REVERT: a 71 MET cc_start: 0.7983 (mmt) cc_final: 0.7749 (mmt) REVERT: a 73 ASN cc_start: 0.8434 (m110) cc_final: 0.8133 (m-40) REVERT: a 74 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: a 145 THR cc_start: 0.8753 (t) cc_final: 0.8442 (p) REVERT: a 244 GLU cc_start: 0.7393 (tt0) cc_final: 0.6935 (tp30) outliers start: 6 outliers final: 3 residues processed: 79 average time/residue: 0.7092 time to fit residues: 58.7494 Evaluate side-chains 78 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 50 PHE Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 7 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107235 restraints weight = 5951.891| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.58 r_work: 0.3143 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7179 Z= 0.146 Angle : 0.625 11.850 9801 Z= 0.295 Chirality : 0.041 0.139 1137 Planarity : 0.005 0.041 1225 Dihedral : 8.968 43.519 1160 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.10 % Allowed : 13.62 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.21 (0.27), residues: 921 helix: 3.42 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -0.65 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 1 48 TYR 0.020 0.001 TYR a 143 PHE 0.018 0.001 PHE 4 70 TRP 0.007 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7179) covalent geometry : angle 0.62545 ( 9801) hydrogen bonds : bond 0.04363 ( 672) hydrogen bonds : angle 4.27011 ( 2010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2581.79 seconds wall clock time: 44 minutes 54.41 seconds (2694.41 seconds total)