Starting phenix.real_space_refine on Thu Nov 14 17:39:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j57_35982/11_2024/8j57_35982.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j57_35982/11_2024/8j57_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j57_35982/11_2024/8j57_35982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j57_35982/11_2024/8j57_35982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j57_35982/11_2024/8j57_35982.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j57_35982/11_2024/8j57_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-5513/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: 7.05, per 1000 atoms: 1.01 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: 1.83 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.56 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: 2.27 Time building geometry restraints manager: 2.01 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: 10.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.140 Find NCS groups from input model: 0.310 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.960 ------------------------------------------------------------------------------- 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= 0.842 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 : 0.714 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: 1.1796 time to fit residues: 123.8133 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 : 0.757 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.854 Fit side-chains REVERT: 8 17 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7873 (mmp) REVERT: a 71 MET cc_start: 0.8724 (mmt) cc_final: 0.8199 (mmt) REVERT: a 74 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8103 (mp10) outliers start: 9 outliers final: 2 residues processed: 93 average time/residue: 1.1749 time to fit residues: 115.4905 Evaluate side-chains 76 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 17 MET 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 43 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 21 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2585 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= 0.201 Angle : 0.614 14.814 9801 Z= 0.299 Chirality : 0.042 0.139 1137 Planarity : 0.005 0.047 1225 Dihedral : 9.486 42.855 1160 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.28), residues: 921 helix: 3.03 (0.18), residues: 777 sheet: None (None), residues: 0 loop : -0.71 (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 0.002 PHE a 63 TYR 0.024 0.001 TYR a 143 ARG 0.008 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 92 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.646 Fit side-chains REVERT: 1 71 MET cc_start: 0.8229 (tmt) cc_final: 0.7787 (tmt) REVERT: 2 50 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.8149 (m-10) REVERT: a 50 LYS cc_start: 0.8324 (mttm) cc_final: 0.8086 (mttp) REVERT: a 71 MET cc_start: 0.8738 (mmt) cc_final: 0.8279 (mmt) REVERT: a 74 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: a 130 ASN cc_start: 0.8157 (m110) cc_final: 0.7894 (m110) outliers start: 15 outliers final: 3 residues processed: 80 average time/residue: 1.2975 time to fit residues: 109.6055 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 : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 7179 Z= 0.247 Angle : 0.622 14.426 9801 Z= 0.303 Chirality : 0.042 0.144 1137 Planarity : 0.005 0.056 1225 Dihedral : 9.443 43.109 1160 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.19 % Allowed : 9.70 % 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: 3.85 (0.28), residues: 921 helix: 3.07 (0.18), residues: 777 sheet: None (None), residues: 0 loop : -0.71 (0.49), 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 0.022 0.002 TYR a 143 ARG 0.011 0.001 ARG 1 48 *********************** 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 94 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.685 Fit side-chains REVERT: a 48 ARG cc_start: 0.7693 (tmt170) cc_final: 0.7031 (ttm170) REVERT: a 50 LYS cc_start: 0.8405 (mttm) cc_final: 0.8178 (mttp) REVERT: a 71 MET cc_start: 0.8714 (mmt) cc_final: 0.8264 (mmt) REVERT: a 74 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7779 (mp10) REVERT: a 82 ARG cc_start: 0.7430 (ttt90) cc_final: 0.7157 (ttm-80) outliers start: 14 outliers final: 5 residues processed: 84 average time/residue: 1.4031 time to fit residues: 123.7148 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 : 0.712 ------------------------------------------------------------------------------- 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 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 69 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2892 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= 0.206 Angle : 0.599 12.307 9801 Z= 0.289 Chirality : 0.041 0.132 1137 Planarity : 0.005 0.048 1225 Dihedral : 9.266 42.446 1160 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.82 % Allowed : 9.55 % Favored : 87.64 % 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: 3.19 (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 0.016 0.001 PHE a 140 TYR 0.021 0.001 TYR a 143 ARG 0.008 0.001 ARG 8 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 90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.653 Fit side-chains REVERT: 1 42 GLN cc_start: 0.8025 (mp10) cc_final: 0.7812 (mp10) REVERT: 2 50 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8110 (m-10) REVERT: a 48 ARG cc_start: 0.7694 (tmt170) cc_final: 0.7163 (ttm170) REVERT: a 50 LYS cc_start: 0.8408 (mttm) cc_final: 0.8196 (mttp) REVERT: a 71 MET cc_start: 0.8707 (mmt) cc_final: 0.8288 (mmt) REVERT: a 74 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: a 82 ARG cc_start: 0.7403 (ttt90) cc_final: 0.7134 (ttm-80) outliers start: 18 outliers final: 5 residues processed: 80 average time/residue: 1.2764 time to fit residues: 107.9424 Evaluate side-chains 75 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 50 PHE Chi-restraints excluded: chain 4 residue 78 THR Chi-restraints excluded: chain 5 residue 71 MET 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 27 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2983 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= 0.228 Angle : 0.611 11.002 9801 Z= 0.293 Chirality : 0.042 0.174 1137 Planarity : 0.005 0.066 1225 Dihedral : 9.249 42.603 1160 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.50 % Allowed : 11.42 % 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 (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: 3.93 (0.28), residues: 921 helix: 2.94 (0.18), residues: 831 sheet: None (None), residues: 0 loop : -1.23 (0.67), 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 0.019 0.001 TYR a 143 ARG 0.008 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: 16 poor density : 73 time to evaluate : 0.669 Fit side-chains REVERT: 1 42 GLN cc_start: 0.8028 (mp10) cc_final: 0.7823 (mp10) REVERT: 1 71 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7759 (tmt) REVERT: a 48 ARG cc_start: 0.7743 (tmt170) cc_final: 0.7221 (ttm170) REVERT: a 71 MET cc_start: 0.8700 (mmt) cc_final: 0.8292 (mmt) REVERT: a 74 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7699 (mp10) REVERT: a 82 ARG cc_start: 0.7427 (ttt90) cc_final: 0.7151 (ttm-80) outliers start: 16 outliers final: 5 residues processed: 79 average time/residue: 1.3904 time to fit residues: 115.5306 Evaluate side-chains 75 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 71 MET Chi-restraints excluded: chain 4 residue 78 THR Chi-restraints excluded: chain 5 residue 71 MET 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 9 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 0.0040 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7179 Z= 0.189 Angle : 0.605 10.474 9801 Z= 0.286 Chirality : 0.041 0.176 1137 Planarity : 0.005 0.073 1225 Dihedral : 9.055 45.545 1160 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.88 % Allowed : 12.21 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.12 (0.28), residues: 921 helix: 3.33 (0.18), residues: 777 sheet: None (None), residues: 0 loop : -1.14 (0.46), residues: 144 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 0.024 0.001 TYR a 131 ARG 0.014 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 91 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.724 Fit side-chains REVERT: 1 42 GLN cc_start: 0.7984 (mp10) cc_final: 0.7720 (mp10) REVERT: 1 71 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7689 (tmt) REVERT: 2 50 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8088 (m-10) REVERT: a 48 ARG cc_start: 0.7665 (tmt170) cc_final: 0.7194 (ttm170) REVERT: a 71 MET cc_start: 0.8671 (mmt) cc_final: 0.8278 (mmt) REVERT: a 74 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: a 82 ARG cc_start: 0.7429 (ttt90) cc_final: 0.7163 (ttm-80) outliers start: 12 outliers final: 5 residues processed: 83 average time/residue: 1.4577 time to fit residues: 127.4570 Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 5 residue 41 ARG 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 24 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7179 Z= 0.327 Angle : 0.651 9.621 9801 Z= 0.316 Chirality : 0.044 0.197 1137 Planarity : 0.006 0.073 1225 Dihedral : 9.401 43.432 1160 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.72 % Allowed : 12.99 % 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: 3.72 (0.28), residues: 921 helix: 3.04 (0.18), residues: 777 sheet: None (None), residues: 0 loop : -1.19 (0.45), residues: 144 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 0.020 0.002 PHE a 140 TYR 0.024 0.002 TYR a 131 ARG 0.016 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 87 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.705 Fit side-chains REVERT: 1 42 GLN cc_start: 0.8031 (mp10) cc_final: 0.7831 (mp10) REVERT: a 48 ARG cc_start: 0.7751 (tmt170) cc_final: 0.7186 (ttm170) REVERT: a 71 MET cc_start: 0.8652 (mmt) cc_final: 0.8226 (mmt) REVERT: a 74 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7742 (mp10) outliers start: 11 outliers final: 5 residues processed: 81 average time/residue: 1.5493 time to fit residues: 131.8299 Evaluate side-chains 78 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 78 THR Chi-restraints excluded: chain 5 residue 71 MET 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 79 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3250 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= 0.194 Angle : 0.603 9.843 9801 Z= 0.287 Chirality : 0.041 0.185 1137 Planarity : 0.005 0.057 1225 Dihedral : 9.061 44.109 1160 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.10 % Allowed : 14.08 % 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 (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: 4.29 (0.27), residues: 921 helix: 3.48 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -0.70 (0.43), residues: 162 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 0.016 0.001 PHE a 140 TYR 0.023 0.001 TYR a 131 ARG 0.013 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 80 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.719 Fit side-chains REVERT: 1 42 GLN cc_start: 0.7995 (mp10) cc_final: 0.7785 (mp10) REVERT: 2 50 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8065 (m-10) REVERT: a 71 MET cc_start: 0.8664 (mmt) cc_final: 0.8251 (mmt) REVERT: a 74 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7694 (mp10) outliers start: 7 outliers final: 4 residues processed: 78 average time/residue: 1.3871 time to fit residues: 114.3015 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 : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 0.0980 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3386 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= 0.194 Angle : 0.607 10.094 9801 Z= 0.289 Chirality : 0.041 0.189 1137 Planarity : 0.005 0.060 1225 Dihedral : 8.920 43.628 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 : 13.93 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.38 (0.27), residues: 921 helix: 3.56 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.79 (0.42), residues: 161 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 0.017 0.001 PHE a 140 TYR 0.024 0.001 TYR a 131 ARG 0.012 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 80 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.679 Fit side-chains REVERT: 1 42 GLN cc_start: 0.7932 (mp10) cc_final: 0.7678 (mp10) REVERT: 2 50 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7995 (m-10) REVERT: a 71 MET cc_start: 0.8612 (mmt) cc_final: 0.8201 (mmt) REVERT: a 74 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8140 (mm110) outliers start: 7 outliers final: 4 residues processed: 77 average time/residue: 1.3805 time to fit residues: 111.8937 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 : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 0.0020 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108725 restraints weight = 5973.776| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.60 r_work: 0.3059 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3479 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= 0.191 Angle : 0.609 10.898 9801 Z= 0.287 Chirality : 0.041 0.188 1137 Planarity : 0.005 0.053 1225 Dihedral : 8.845 43.846 1160 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.10 % Allowed : 14.55 % Favored : 84.35 % 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: 4.42 (0.27), residues: 921 helix: 3.58 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.77 (0.43), residues: 161 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 0.017 0.001 PHE a 140 TYR 0.022 0.001 TYR a 131 ARG 0.009 0.001 ARG 1 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2850.47 seconds wall clock time: 52 minutes 20.16 seconds (3140.16 seconds total)