Starting phenix.real_space_refine on Wed Mar 12 00:22:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j57_35982/03_2025/8j57_35982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j57_35982/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j57_35982/03_2025/8j57_35982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j57_35982/03_2025/8j57_35982.map" model { file = "/net/cci-nas-00/data/ceres_data/8j57_35982/03_2025/8j57_35982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j57_35982/03_2025/8j57_35982.cif" } resolution = 2.85 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= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.74, per 1000 atoms: 0.96 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: 1.81 Conformation dependent library (CDL) restraints added in 998.5 milliseconds 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: 0.53 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: 2.13 Time building geometry restraints manager: 2.11 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: 0.010 Normalize map: mean=0, sd=1: 10.920 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.980 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.870 ------------------------------------------------------------------------------- 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= 0.842 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 (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: -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 TRP 0.099 0.026 TRP a 216 HIS 0.007 0.002 HIS a 15 PHE 0.059 0.014 PHE a 192 TYR 0.083 0.012 TYR a 111 ARG 0.007 0.001 ARG 5 48 *********************** 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 : 0.687 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: 1.1058 time to fit residues: 116.0796 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 : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 42 GLN ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109606 restraints weight = 6057.254| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.58 r_work: 0.3129 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2087 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= 0.231 Angle : 0.658 14.741 9801 Z= 0.329 Chirality : 0.044 0.143 1137 Planarity : 0.005 0.056 1225 Dihedral : 10.068 43.534 1160 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.41 % Allowed : 7.82 % Favored : 90.77 % 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: 3.14 (0.28), residues: 921 helix: 2.56 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -0.73 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 216 HIS 0.002 0.001 HIS a 15 PHE 0.020 0.002 PHE a 192 TYR 0.028 0.002 TYR a 143 ARG 0.008 0.001 ARG 7 48 *********************** 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 : 0.698 Fit side-chains REVERT: 4 71 MET cc_start: 0.8488 (tmm) cc_final: 0.8148 (tmm) REVERT: 5 71 MET cc_start: 0.8698 (tmm) cc_final: 0.8375 (tmm) REVERT: a 71 MET cc_start: 0.8139 (mmt) cc_final: 0.7751 (mmt) REVERT: a 74 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: a 244 GLU cc_start: 0.7333 (tt0) cc_final: 0.6869 (tp30) outliers start: 9 outliers final: 2 residues processed: 93 average time/residue: 1.1363 time to fit residues: 111.8992 Evaluate side-chains 75 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 27 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 33 optimal weight: 0.0370 chunk 10 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 82 optimal weight: 0.0030 overall best weight: 0.3668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 46 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 = 0.3704 r_free = 0.3704 target = 0.144666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109642 restraints weight = 6096.102| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.60 r_work: 0.3167 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2646 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= 0.177 Angle : 0.598 14.768 9801 Z= 0.289 Chirality : 0.041 0.139 1137 Planarity : 0.005 0.047 1225 Dihedral : 9.401 42.843 1160 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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 (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: 3.92 (0.28), residues: 921 helix: 3.13 (0.18), residues: 777 sheet: None (None), residues: 0 loop : -0.74 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 PHE 0.019 0.001 PHE a 63 TYR 0.025 0.001 TYR a 143 ARG 0.006 0.001 ARG 7 48 *********************** 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 93 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.651 Fit side-chains REVERT: 4 50 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8486 (m-10) REVERT: 4 71 MET cc_start: 0.8469 (tmm) cc_final: 0.8099 (tmm) REVERT: 5 71 MET cc_start: 0.8671 (tmm) cc_final: 0.8260 (tmm) REVERT: a 71 MET cc_start: 0.8118 (mmt) cc_final: 0.7806 (mmt) REVERT: a 74 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.6721 (mp10) REVERT: a 130 ASN cc_start: 0.7695 (m110) cc_final: 0.7330 (m110) REVERT: a 244 GLU cc_start: 0.7283 (tt0) cc_final: 0.6834 (tp30) outliers start: 15 outliers final: 3 residues processed: 81 average time/residue: 1.1325 time to fit residues: 97.2383 Evaluate side-chains 71 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 65 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 0.0170 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 = 0.141767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106621 restraints weight = 6111.439| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.61 r_work: 0.3134 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7179 Z= 0.208 Angle : 0.603 14.417 9801 Z= 0.290 Chirality : 0.041 0.135 1137 Planarity : 0.005 0.046 1225 Dihedral : 9.305 42.597 1160 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.35 % Allowed : 9.70 % Favored : 87.95 % 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: 3.97 (0.28), residues: 921 helix: 2.96 (0.18), residues: 831 sheet: None (None), residues: 0 loop : -1.13 (0.69), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 PHE 0.017 0.001 PHE a 140 TYR 0.022 0.001 TYR a 143 ARG 0.006 0.001 ARG a 150 *********************** 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 92 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.724 Fit side-chains REVERT: 2 50 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.8171 (m-10) REVERT: 4 71 MET cc_start: 0.8504 (tmm) cc_final: 0.8068 (tmm) REVERT: 5 71 MET cc_start: 0.8645 (tmm) cc_final: 0.8299 (tmm) REVERT: a 48 ARG cc_start: 0.7875 (tmt170) cc_final: 0.6681 (ttm170) REVERT: a 71 MET cc_start: 0.8104 (mmt) cc_final: 0.7773 (mmt) REVERT: a 74 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7210 (mp10) REVERT: a 130 ASN cc_start: 0.7693 (m110) cc_final: 0.7353 (m110) REVERT: a 244 GLU cc_start: 0.7282 (tt0) cc_final: 0.6845 (tp30) outliers start: 15 outliers final: 5 residues processed: 81 average time/residue: 1.3475 time to fit residues: 115.0007 Evaluate side-chains 79 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain a residue 122 LEU 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 0 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.143382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.108908 restraints weight = 5942.633| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.57 r_work: 0.3121 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7179 Z= 0.236 Angle : 0.611 12.234 9801 Z= 0.296 Chirality : 0.042 0.141 1137 Planarity : 0.005 0.058 1225 Dihedral : 9.306 42.788 1160 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.50 % Allowed : 10.17 % 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 (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: 3.92 (0.28), residues: 921 helix: 3.15 (0.18), residues: 777 sheet: None (None), residues: 0 loop : -0.90 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 PHE 0.018 0.002 PHE a 140 TYR 0.021 0.001 TYR a 143 ARG 0.011 0.001 ARG 1 48 *********************** 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 87 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.632 Fit side-chains REVERT: 1 42 GLN cc_start: 0.7604 (mp10) cc_final: 0.7276 (mp10) REVERT: 1 71 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7626 (tmt) REVERT: 2 50 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8144 (m-10) REVERT: 3 48 ARG cc_start: 0.8389 (mtm110) cc_final: 0.8096 (ttp-170) REVERT: 4 71 MET cc_start: 0.8493 (tmm) cc_final: 0.8022 (tmm) REVERT: 5 71 MET cc_start: 0.8646 (tmm) cc_final: 0.8368 (tmm) REVERT: a 48 ARG cc_start: 0.7920 (tmt170) cc_final: 0.6782 (ttm170) REVERT: a 71 MET cc_start: 0.8062 (mmt) cc_final: 0.7765 (mmt) REVERT: a 74 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: a 82 ARG cc_start: 0.7789 (ttt90) cc_final: 0.7456 (ttm-80) REVERT: a 130 ASN cc_start: 0.7665 (m110) cc_final: 0.7402 (m-40) REVERT: a 244 GLU cc_start: 0.7304 (tt0) cc_final: 0.6844 (tp30) outliers start: 16 outliers final: 5 residues processed: 77 average time/residue: 1.3010 time to fit residues: 105.5815 Evaluate side-chains 74 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 71 MET Chi-restraints excluded: chain 2 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 56 VAL Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 122 LEU 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 62 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 80 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: 7 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106439 restraints weight = 6026.823| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.61 r_work: 0.3142 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7179 Z= 0.203 Angle : 0.594 10.905 9801 Z= 0.284 Chirality : 0.041 0.131 1137 Planarity : 0.005 0.044 1225 Dihedral : 9.176 44.761 1160 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.66 % Allowed : 10.80 % Favored : 86.54 % 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: 4.06 (0.27), residues: 921 helix: 3.26 (0.18), residues: 777 sheet: None (None), residues: 0 loop : -0.97 (0.46), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 PHE 0.017 0.001 PHE a 140 TYR 0.020 0.001 TYR a 143 ARG 0.009 0.001 ARG 7 48 *********************** 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 89 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.613 Fit side-chains REVERT: 1 42 GLN cc_start: 0.7597 (mp10) cc_final: 0.7273 (mp10) REVERT: 1 71 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7560 (tmt) REVERT: 2 50 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8143 (m-10) REVERT: 4 71 MET cc_start: 0.8460 (tmm) cc_final: 0.7982 (tmm) REVERT: 5 71 MET cc_start: 0.8629 (tmm) cc_final: 0.8237 (tmm) REVERT: a 48 ARG cc_start: 0.7940 (tmt170) cc_final: 0.6875 (ttm170) REVERT: a 50 LYS cc_start: 0.7528 (mttp) cc_final: 0.7184 (mttp) REVERT: a 71 MET cc_start: 0.8043 (mmt) cc_final: 0.7756 (mmt) REVERT: a 74 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7082 (mp10) REVERT: a 82 ARG cc_start: 0.7735 (ttt90) cc_final: 0.7406 (ttm-80) REVERT: a 145 THR cc_start: 0.8689 (t) cc_final: 0.8404 (p) REVERT: a 244 GLU cc_start: 0.7361 (tt0) cc_final: 0.6890 (tp30) outliers start: 17 outliers final: 4 residues processed: 79 average time/residue: 1.1870 time to fit residues: 99.2313 Evaluate side-chains 74 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 71 MET Chi-restraints excluded: chain 2 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 56 VAL Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 48 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 0.0020 chunk 54 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 70 optimal weight: 0.0040 chunk 77 optimal weight: 0.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.144779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.109767 restraints weight = 5974.059| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.60 r_work: 0.3183 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3260 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= 0.174 Angle : 0.578 10.201 9801 Z= 0.274 Chirality : 0.040 0.128 1137 Planarity : 0.004 0.042 1225 Dihedral : 8.944 48.713 1160 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.72 % Allowed : 12.52 % 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 (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: 4.63 (0.27), residues: 921 helix: 3.67 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -0.32 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 216 HIS 0.004 0.001 HIS a 144 PHE 0.016 0.001 PHE a 140 TYR 0.019 0.001 TYR a 143 ARG 0.007 0.001 ARG 1 48 *********************** 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 90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.683 Fit side-chains REVERT: 1 42 GLN cc_start: 0.7602 (mp10) cc_final: 0.7211 (mp10) REVERT: 1 71 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7530 (tmt) REVERT: 2 50 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8130 (m-10) REVERT: 4 71 MET cc_start: 0.8511 (tmm) cc_final: 0.8173 (tmm) REVERT: 5 71 MET cc_start: 0.8649 (tmm) cc_final: 0.8297 (tmm) REVERT: 7 54 PHE cc_start: 0.8398 (m-80) cc_final: 0.8159 (m-80) REVERT: a 48 ARG cc_start: 0.7827 (tmt170) cc_final: 0.6759 (ttm170) REVERT: a 50 LYS cc_start: 0.7581 (mttp) cc_final: 0.7201 (mttp) REVERT: a 71 MET cc_start: 0.8041 (mmt) cc_final: 0.7768 (mmt) REVERT: a 145 THR cc_start: 0.8722 (t) cc_final: 0.8432 (p) REVERT: a 244 GLU cc_start: 0.7373 (tt0) cc_final: 0.6923 (tp30) outliers start: 11 outliers final: 4 residues processed: 83 average time/residue: 1.2309 time to fit residues: 108.3746 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 : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 71 MET Chi-restraints excluded: chain 2 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 56 VAL 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 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.141518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106414 restraints weight = 5962.520| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.60 r_work: 0.3137 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7179 Z= 0.215 Angle : 0.591 10.082 9801 Z= 0.284 Chirality : 0.041 0.137 1137 Planarity : 0.005 0.040 1225 Dihedral : 9.017 44.349 1160 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.41 % Allowed : 13.30 % 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 (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: 4.13 (0.28), residues: 921 helix: 3.10 (0.18), residues: 831 sheet: None (None), residues: 0 loop : -1.50 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 PHE 0.017 0.001 PHE a 140 TYR 0.020 0.001 TYR a 143 ARG 0.006 0.001 ARG 1 48 *********************** 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 83 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.693 Fit side-chains REVERT: 1 71 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7614 (tmt) REVERT: 2 50 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8096 (m-10) REVERT: 4 71 MET cc_start: 0.8639 (tmm) cc_final: 0.8229 (tmm) REVERT: 5 71 MET cc_start: 0.8664 (tmm) cc_final: 0.8319 (tmm) REVERT: a 48 ARG cc_start: 0.7857 (tmt170) cc_final: 0.6780 (ttm170) REVERT: a 71 MET cc_start: 0.7982 (mmt) cc_final: 0.7733 (mmt) REVERT: a 244 GLU cc_start: 0.7336 (tt0) cc_final: 0.6885 (tp30) outliers start: 9 outliers final: 4 residues processed: 79 average time/residue: 1.2065 time to fit residues: 100.8298 Evaluate side-chains 76 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 71 MET Chi-restraints excluded: chain 2 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 56 VAL 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 3 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.0020 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.142810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.107736 restraints weight = 6077.901| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.61 r_work: 0.3003 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7179 Z= 0.200 Angle : 0.598 11.872 9801 Z= 0.283 Chirality : 0.041 0.130 1137 Planarity : 0.005 0.040 1225 Dihedral : 8.948 46.689 1160 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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 (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: 4.46 (0.28), residues: 921 helix: 3.31 (0.18), residues: 813 sheet: None (None), residues: 0 loop : -0.40 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 PHE 0.016 0.001 PHE a 140 TYR 0.020 0.001 TYR a 143 ARG 0.005 0.001 ARG 1 48 *********************** 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 78 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.671 Fit side-chains REVERT: 1 71 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7381 (tmt) REVERT: 2 50 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7905 (m-10) REVERT: 4 71 MET cc_start: 0.8497 (tmm) cc_final: 0.8075 (tmm) REVERT: 5 71 MET cc_start: 0.8505 (tmm) cc_final: 0.8119 (tmm) REVERT: 7 54 PHE cc_start: 0.8240 (m-80) cc_final: 0.8020 (m-80) REVERT: a 48 ARG cc_start: 0.7768 (tmt170) cc_final: 0.6676 (ttm170) REVERT: a 145 THR cc_start: 0.8607 (t) cc_final: 0.8297 (p) REVERT: a 244 GLU cc_start: 0.7233 (tt0) cc_final: 0.6757 (tp30) outliers start: 7 outliers final: 3 residues processed: 74 average time/residue: 1.2525 time to fit residues: 97.8296 Evaluate side-chains 74 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 0.0370 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 0.0040 chunk 40 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.4672 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.144226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109191 restraints weight = 6070.009| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.62 r_work: 0.3062 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7179 Z= 0.187 Angle : 0.593 12.076 9801 Z= 0.281 Chirality : 0.041 0.140 1137 Planarity : 0.004 0.041 1225 Dihedral : 8.838 48.645 1160 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.78 % Allowed : 13.62 % Favored : 85.60 % 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: 4.52 (0.27), residues: 921 helix: 3.35 (0.18), residues: 813 sheet: None (None), residues: 0 loop : -0.41 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 216 HIS 0.004 0.001 HIS a 144 PHE 0.016 0.001 PHE a 140 TYR 0.019 0.001 TYR a 143 ARG 0.005 0.001 ARG 1 48 ********************** 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 79 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.672 Fit side-chains REVERT: 1 71 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7475 (tmt) REVERT: 2 50 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8053 (m-10) REVERT: 4 71 MET cc_start: 0.8570 (tmm) cc_final: 0.8183 (tmm) REVERT: 5 71 MET cc_start: 0.8555 (tmm) cc_final: 0.8187 (tmm) REVERT: 7 54 PHE cc_start: 0.8298 (m-80) cc_final: 0.8084 (m-80) REVERT: a 145 THR cc_start: 0.8688 (t) cc_final: 0.8380 (p) REVERT: a 244 GLU cc_start: 0.7295 (tt0) cc_final: 0.6820 (tp30) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 1.2108 time to fit residues: 98.8698 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 : 0.640 ------------------------------------------------------------------------------- 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 109 VAL Chi-restraints excluded: chain a residue 124 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 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 = 0.3683 r_free = 0.3683 target = 0.142581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107425 restraints weight = 6027.274| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.61 r_work: 0.3064 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7179 Z= 0.216 Angle : 0.602 10.527 9801 Z= 0.288 Chirality : 0.041 0.137 1137 Planarity : 0.005 0.069 1225 Dihedral : 8.936 45.881 1160 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.10 % Allowed : 13.30 % Favored : 85.60 % 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: 4.34 (0.27), residues: 921 helix: 3.49 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -0.51 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 216 HIS 0.003 0.001 HIS a 144 PHE 0.017 0.001 PHE a 140 TYR 0.020 0.001 TYR a 143 ARG 0.010 0.001 ARG 1 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4732.77 seconds wall clock time: 81 minutes 29.97 seconds (4889.97 seconds total)