Starting phenix.real_space_refine on Fri Apr 5 20:57:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul3_26590/04_2024/7ul3_26590_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul3_26590/04_2024/7ul3_26590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul3_26590/04_2024/7ul3_26590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul3_26590/04_2024/7ul3_26590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul3_26590/04_2024/7ul3_26590_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul3_26590/04_2024/7ul3_26590_updated.pdb" } resolution = 3.0 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 3570 2.51 5 N 910 2.21 5 O 973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5484 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1944 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 7, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 107 Chain: "C" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 807 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "H" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1300 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 9 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "L" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1413 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 189} Chain breaks: 4 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FO9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.69, per 1000 atoms: 0.67 Number of scatterers: 5484 At special positions: 0 Unit cell: (65.9452, 80.6961, 157.921, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 973 8.00 N 910 7.00 C 3570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.92 Conformation dependent library (CDL) restraints added in 1.0 seconds 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 12 sheets defined 31.6% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 17 through 45 Processing helix chain 'A' and resid 52 through 69 removed outlier: 4.504A pdb=" N PHE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 Processing helix chain 'A' and resid 88 through 103 removed outlier: 3.632A pdb=" N ILE A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 126 through 129 No H-bonds generated for 'chain 'A' and resid 126 through 129' Processing helix chain 'A' and resid 132 through 154 Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.590A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 211 removed outlier: 3.541A pdb=" N LEU A 196 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 260 Proline residue: A 249 - end of helix removed outlier: 3.527A pdb=" N GLY A 258 " --> pdb=" O PHE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 291 removed outlier: 3.746A pdb=" N VAL A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N SER A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 99 through 100B No H-bonds generated for 'chain 'H' and resid 99 through 100B' Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 183 through 188 Processing sheet with id= A, first strand: chain 'C' and resid 5 through 9 removed outlier: 3.596A pdb=" N GLN C 5 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 27 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER C 23 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 81 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 72 " --> pdb=" O TYR C 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 59 through 61 removed outlier: 6.893A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER C 52 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET C 36 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N THR C 54 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N TYR C 34 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU C 100 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET C 36 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN C 98 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TRP C 38 " --> pdb=" O TYR C 96 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR C 96 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG C 40 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL C 94 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 98 through 102 Processing sheet with id= D, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.699A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 107 through 109 removed outlier: 3.663A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.509A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 151 through 153 Processing sheet with id= H, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.248A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ALA L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLU L 105 " --> pdb=" O ALA L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'L' and resid 21 through 24 removed outlier: 4.046A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 85 through 89 removed outlier: 5.900A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.790A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 145 through 150 removed outlier: 3.824A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 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: 1.15 - 1.29: 860 1.29 - 1.42: 1508 1.42 - 1.56: 3189 1.56 - 1.69: 3 1.69 - 1.83: 38 Bond restraints: 5598 Sorted by residual: bond pdb=" C5 FO9 A 401 " pdb=" S1 FO9 A 401 " ideal model delta sigma weight residual 1.802 1.541 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C6 FO9 A 401 " pdb=" S1 FO9 A 401 " ideal model delta sigma weight residual 1.771 1.550 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C4 FO9 A 401 " pdb=" N4 FO9 A 401 " ideal model delta sigma weight residual 1.284 1.452 -0.168 2.00e-02 2.50e+03 7.02e+01 bond pdb=" C4 FO9 A 401 " pdb=" C5 FO9 A 401 " ideal model delta sigma weight residual 1.516 1.377 0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C THR L 74 " pdb=" O THR L 74 " ideal model delta sigma weight residual 1.234 1.154 0.080 1.22e-02 6.72e+03 4.30e+01 ... (remaining 5593 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.00: 115 106.00 - 113.00: 3046 113.00 - 120.00: 1836 120.00 - 126.99: 2600 126.99 - 133.99: 72 Bond angle restraints: 7669 Sorted by residual: angle pdb=" CA LEU L 73 " pdb=" C LEU L 73 " pdb=" N THR L 74 " ideal model delta sigma weight residual 115.51 123.82 -8.31 1.24e+00 6.50e-01 4.49e+01 angle pdb=" C THR L 22 " pdb=" CA THR L 22 " pdb=" CB THR L 22 " ideal model delta sigma weight residual 109.65 99.01 10.64 1.75e+00 3.27e-01 3.70e+01 angle pdb=" C2 FO9 A 401 " pdb=" S FO9 A 401 " pdb=" C3 FO9 A 401 " ideal model delta sigma weight residual 97.71 115.60 -17.89 3.00e+00 1.11e-01 3.56e+01 angle pdb=" CA THR L 74 " pdb=" C THR L 74 " pdb=" O THR L 74 " ideal model delta sigma weight residual 120.99 114.46 6.53 1.12e+00 7.97e-01 3.40e+01 angle pdb=" O FO9 A 401 " pdb=" S2 FO9 A 401 " pdb=" O1 FO9 A 401 " ideal model delta sigma weight residual 116.54 99.19 17.35 3.00e+00 1.11e-01 3.35e+01 ... (remaining 7664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 3020 17.79 - 35.58: 161 35.58 - 53.37: 27 53.37 - 71.15: 7 71.15 - 88.94: 1 Dihedral angle restraints: 3216 sinusoidal: 997 harmonic: 2219 Sorted by residual: dihedral pdb=" CB CYS A 91 " pdb=" SG CYS A 91 " pdb=" SG CYS A 174 " pdb=" CB CYS A 174 " ideal model delta sinusoidal sigma weight residual -86.00 -156.31 70.31 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" C THR L 22 " pdb=" N THR L 22 " pdb=" CA THR L 22 " pdb=" CB THR L 22 " ideal model delta harmonic sigma weight residual -122.00 -108.53 -13.47 0 2.50e+00 1.60e-01 2.90e+01 dihedral pdb=" C THR L 20 " pdb=" N THR L 20 " pdb=" CA THR L 20 " pdb=" CB THR L 20 " ideal model delta harmonic sigma weight residual -122.00 -111.45 -10.55 0 2.50e+00 1.60e-01 1.78e+01 ... (remaining 3213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 700 0.047 - 0.093: 174 0.093 - 0.140: 47 0.140 - 0.187: 2 0.187 - 0.233: 5 Chirality restraints: 928 Sorted by residual: chirality pdb=" CA THR L 22 " pdb=" N THR L 22 " pdb=" C THR L 22 " pdb=" CB THR L 22 " both_signs ideal model delta sigma weight residual False 2.53 2.76 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA LEU L 73 " pdb=" N LEU L 73 " pdb=" C LEU L 73 " pdb=" CB LEU L 73 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA THR L 74 " pdb=" N THR L 74 " pdb=" C THR L 74 " pdb=" CB THR L 74 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 925 not shown) Planarity restraints: 952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 284 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 285 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR L 72 " 0.023 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C THR L 72 " -0.076 2.00e-02 2.50e+03 pdb=" O THR L 72 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU L 73 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 FO9 A 401 " -0.038 2.00e-02 2.50e+03 3.01e-02 1.81e+01 pdb=" C6 FO9 A 401 " 0.028 2.00e-02 2.50e+03 pdb=" C7 FO9 A 401 " -0.002 2.00e-02 2.50e+03 pdb=" N1 FO9 A 401 " 0.019 2.00e-02 2.50e+03 pdb=" N2 FO9 A 401 " -0.050 2.00e-02 2.50e+03 pdb=" N3 FO9 A 401 " 0.039 2.00e-02 2.50e+03 pdb=" N4 FO9 A 401 " -0.015 2.00e-02 2.50e+03 pdb=" S1 FO9 A 401 " 0.019 2.00e-02 2.50e+03 ... (remaining 949 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 506 2.75 - 3.29: 5135 3.29 - 3.82: 8560 3.82 - 4.36: 9676 4.36 - 4.90: 17581 Nonbonded interactions: 41458 Sorted by model distance: nonbonded pdb=" N PHE C 31 " pdb=" O ARG C 102 " model vdw 2.211 2.520 nonbonded pdb=" O ARG A 213 " pdb=" NH2 ARG C 102 " model vdw 2.324 2.520 nonbonded pdb=" OD1 ASP H 101 " pdb=" N TYR H 102 " model vdw 2.355 2.520 nonbonded pdb=" O ASN A 280 " pdb=" OD1 ASN A 280 " model vdw 2.364 3.040 nonbonded pdb=" NH1 ARG A 230 " pdb=" O ILE C 105 " model vdw 2.388 2.520 ... (remaining 41453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 11.480 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.830 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 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 : 0.007 0.261 5598 Z= 0.520 Angle : 0.876 17.894 7669 Z= 0.482 Chirality : 0.046 0.233 928 Planarity : 0.007 0.114 952 Dihedral : 11.481 88.942 1768 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.30), residues: 727 helix: 2.31 (0.32), residues: 228 sheet: 1.24 (0.36), residues: 198 loop : -0.34 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 100G HIS 0.010 0.002 HIS H 200 PHE 0.019 0.002 PHE A 191 TYR 0.028 0.002 TYR C 81 ARG 0.005 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.732 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.6888 time to fit residues: 48.0136 Evaluate side-chains 41 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 31 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.0050 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 67 optimal weight: 20.0000 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN H 200 HIS L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5506 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5598 Z= 0.158 Angle : 0.532 6.324 7669 Z= 0.279 Chirality : 0.041 0.136 928 Planarity : 0.005 0.068 952 Dihedral : 4.984 59.290 821 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.25 % Allowed : 8.18 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.31), residues: 727 helix: 2.64 (0.32), residues: 233 sheet: 1.72 (0.35), residues: 206 loop : -0.41 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 275 HIS 0.002 0.001 HIS L 189 PHE 0.012 0.001 PHE H 27 TYR 0.016 0.002 TYR A 78 ARG 0.007 0.001 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.549 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 43 average time/residue: 0.7437 time to fit residues: 34.8956 Evaluate side-chains 37 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 66 optimal weight: 6.9990 chunk 22 optimal weight: 0.1980 chunk 54 optimal weight: 20.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5762 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5598 Z= 0.316 Angle : 0.594 6.563 7669 Z= 0.315 Chirality : 0.044 0.144 928 Planarity : 0.005 0.057 952 Dihedral : 5.209 56.037 821 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.48 % Allowed : 10.63 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.31), residues: 727 helix: 1.94 (0.33), residues: 240 sheet: 1.58 (0.36), residues: 202 loop : -0.56 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 275 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.002 PHE H 27 TYR 0.019 0.002 TYR A 94 ARG 0.003 0.001 ARG C 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 38 time to evaluate : 0.580 Fit side-chains REVERT: A 151 PHE cc_start: 0.7397 (m-80) cc_final: 0.7188 (m-80) outliers start: 17 outliers final: 8 residues processed: 48 average time/residue: 0.6177 time to fit residues: 32.7320 Evaluate side-chains 46 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 34 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 71 optimal weight: 50.0000 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN H 39 GLN L 38 GLN L 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5598 Z= 0.331 Angle : 0.590 5.570 7669 Z= 0.317 Chirality : 0.044 0.145 928 Planarity : 0.005 0.049 952 Dihedral : 5.160 47.547 821 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.89 % Allowed : 12.27 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.89 (0.31), residues: 727 helix: 1.55 (0.33), residues: 240 sheet: 1.49 (0.35), residues: 207 loop : -0.98 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 35 HIS 0.003 0.001 HIS L 189 PHE 0.018 0.002 PHE H 27 TYR 0.018 0.002 TYR A 126 ARG 0.002 0.001 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 42 time to evaluate : 0.560 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 55 average time/residue: 0.5792 time to fit residues: 37.9691 Evaluate side-chains 50 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 40.0000 chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5825 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5598 Z= 0.282 Angle : 0.552 5.583 7669 Z= 0.294 Chirality : 0.042 0.144 928 Planarity : 0.004 0.044 952 Dihedral : 4.872 41.207 821 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.68 % Allowed : 13.09 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.79 (0.31), residues: 727 helix: 1.64 (0.34), residues: 239 sheet: 1.13 (0.36), residues: 210 loop : -0.95 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 35 HIS 0.002 0.001 HIS L 189 PHE 0.016 0.002 PHE H 27 TYR 0.015 0.002 TYR A 250 ARG 0.007 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 42 time to evaluate : 0.602 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 56 average time/residue: 0.5916 time to fit residues: 36.6465 Evaluate side-chains 55 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 50.0000 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5792 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5598 Z= 0.203 Angle : 0.509 5.610 7669 Z= 0.267 Chirality : 0.040 0.134 928 Planarity : 0.004 0.039 952 Dihedral : 4.547 38.546 821 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.27 % Allowed : 14.72 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.31), residues: 727 helix: 1.82 (0.34), residues: 239 sheet: 1.23 (0.37), residues: 214 loop : -0.87 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 275 HIS 0.002 0.001 HIS L 189 PHE 0.013 0.001 PHE H 27 TYR 0.016 0.001 TYR A 78 ARG 0.004 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 0.591 Fit side-chains REVERT: A 94 TYR cc_start: 0.6878 (OUTLIER) cc_final: 0.5597 (t80) REVERT: A 186 ASP cc_start: 0.6684 (t70) cc_final: 0.6462 (t0) REVERT: H 4 LEU cc_start: 0.4532 (OUTLIER) cc_final: 0.4217 (mt) outliers start: 16 outliers final: 12 residues processed: 51 average time/residue: 0.5847 time to fit residues: 33.0318 Evaluate side-chains 53 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 GLN C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 5598 Z= 0.450 Angle : 0.649 6.576 7669 Z= 0.350 Chirality : 0.046 0.162 928 Planarity : 0.005 0.040 952 Dihedral : 5.169 43.250 821 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.29 % Allowed : 14.93 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.28 (0.30), residues: 727 helix: 1.22 (0.33), residues: 239 sheet: 0.80 (0.35), residues: 220 loop : -1.30 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 35 HIS 0.003 0.001 HIS H 100B PHE 0.019 0.002 PHE H 27 TYR 0.022 0.003 TYR L 49 ARG 0.004 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 41 time to evaluate : 0.663 Fit side-chains REVERT: A 94 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.5820 (t80) REVERT: A 186 ASP cc_start: 0.6939 (t70) cc_final: 0.6720 (t0) REVERT: C 36 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.5816 (mmm) REVERT: H 4 LEU cc_start: 0.4277 (OUTLIER) cc_final: 0.3983 (mt) outliers start: 21 outliers final: 13 residues processed: 56 average time/residue: 0.6188 time to fit residues: 38.0841 Evaluate side-chains 56 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5820 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5598 Z= 0.209 Angle : 0.509 5.544 7669 Z= 0.270 Chirality : 0.040 0.136 928 Planarity : 0.004 0.037 952 Dihedral : 4.665 37.778 821 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.68 % Allowed : 16.16 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.61 (0.31), residues: 727 helix: 1.66 (0.34), residues: 238 sheet: 0.99 (0.36), residues: 214 loop : -1.23 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.001 PHE H 27 TYR 0.014 0.002 TYR A 78 ARG 0.003 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 44 time to evaluate : 0.624 Fit side-chains REVERT: A 94 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.5592 (t80) REVERT: H 4 LEU cc_start: 0.4358 (OUTLIER) cc_final: 0.4142 (mt) outliers start: 18 outliers final: 14 residues processed: 57 average time/residue: 0.5286 time to fit residues: 33.5902 Evaluate side-chains 59 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 40.0000 chunk 68 optimal weight: 20.0000 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 70 optimal weight: 30.0000 chunk 42 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.5827 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5598 Z= 0.224 Angle : 0.509 5.564 7669 Z= 0.272 Chirality : 0.040 0.134 928 Planarity : 0.004 0.037 952 Dihedral : 4.601 39.423 821 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.27 % Allowed : 16.16 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.75 (0.31), residues: 727 helix: 1.78 (0.34), residues: 238 sheet: 1.04 (0.36), residues: 214 loop : -1.14 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 275 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE H 27 TYR 0.014 0.001 TYR A 250 ARG 0.003 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.586 Fit side-chains REVERT: A 94 TYR cc_start: 0.6887 (OUTLIER) cc_final: 0.5622 (t80) REVERT: C 117 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7233 (p) REVERT: H 4 LEU cc_start: 0.4352 (OUTLIER) cc_final: 0.4147 (mt) outliers start: 16 outliers final: 13 residues processed: 55 average time/residue: 0.5790 time to fit residues: 35.2035 Evaluate side-chains 56 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 58 optimal weight: 0.0870 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5598 Z= 0.252 Angle : 0.526 5.596 7669 Z= 0.280 Chirality : 0.041 0.137 928 Planarity : 0.004 0.037 952 Dihedral : 4.689 41.997 821 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.68 % Allowed : 15.34 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.68 (0.31), residues: 727 helix: 1.71 (0.34), residues: 238 sheet: 0.99 (0.36), residues: 214 loop : -1.14 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 275 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.002 PHE H 27 TYR 0.018 0.002 TYR A 202 ARG 0.003 0.000 ARG L 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 39 time to evaluate : 0.538 Fit side-chains REVERT: A 94 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.5647 (t80) REVERT: H 4 LEU cc_start: 0.4362 (OUTLIER) cc_final: 0.4151 (mt) outliers start: 18 outliers final: 15 residues processed: 51 average time/residue: 0.5324 time to fit residues: 30.0422 Evaluate side-chains 56 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 39 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4812 r_free = 0.4812 target = 0.239929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.163789 restraints weight = 7024.902| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.54 r_work: 0.3905 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5598 Z= 0.338 Angle : 0.574 5.933 7669 Z= 0.308 Chirality : 0.043 0.145 928 Planarity : 0.004 0.037 952 Dihedral : 4.922 45.055 821 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.68 % Allowed : 15.54 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.51 (0.31), residues: 727 helix: 1.59 (0.34), residues: 235 sheet: 0.84 (0.36), residues: 223 loop : -1.24 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 100E HIS 0.003 0.001 HIS H 35 PHE 0.015 0.002 PHE C 39 TYR 0.017 0.002 TYR A 250 ARG 0.003 0.001 ARG H 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.98 seconds wall clock time: 33 minutes 14.54 seconds (1994.54 seconds total)