Starting phenix.real_space_refine on Tue Feb 13 12:34:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl6_27497/02_2024/8dl6_27497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl6_27497/02_2024/8dl6_27497.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/8dl6_27497/02_2024/8dl6_27497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl6_27497/02_2024/8dl6_27497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl6_27497/02_2024/8dl6_27497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl6_27497/02_2024/8dl6_27497.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= 0.014 sd= 0.076 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 Ca 1 9.91 5 S 34 5.16 5 C 3944 2.51 5 N 1045 2.21 5 O 1147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 52": "OE1" <-> "OE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A ARG 540": "NH1" <-> "NH2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C ASP 102": "OD1" <-> "OD2" Residue "C ASP 105": "OD1" <-> "OD2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 92": "OD1" <-> "OD2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 127": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6171 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 442, 3377 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 442, 3377 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 3439 Chain: "C" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1348 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 177 Chain: "D" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1437 Classifications: {'peptide': 219} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 81} Link IDs: {'PTRANS': 14, 'TRANS': 204} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATHR A 334 " occ=0.71 ... (12 atoms not shown) pdb=" CG2BTHR A 334 " occ=0.29 Time building chain proxies: 5.41, per 1000 atoms: 0.88 Number of scatterers: 6171 At special positions: 0 Unit cell: (75.9, 72.6, 141.9, 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) Ca 1 19.99 S 34 16.00 O 1147 8.00 N 1045 7.00 C 3944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 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: 2.42 Conformation dependent library (CDL) restraints added in 2.2 seconds 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 9 sheets defined 49.9% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 15 through 23 Processing helix chain 'A' and resid 24 through 55 removed outlier: 4.066A pdb=" N LEU A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 85 removed outlier: 3.882A pdb=" N VAL A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 116 through 124 removed outlier: 4.664A pdb=" N TYR A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 163 removed outlier: 4.387A pdb=" N THR A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 197 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 228 removed outlier: 3.911A pdb=" N GLY A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 6.527A pdb=" N ALA A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 305 Processing helix chain 'A' and resid 307 through 317 removed outlier: 3.523A pdb=" N ALA A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 340 through 368 removed outlier: 3.628A pdb=" N ILE A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 393 removed outlier: 3.583A pdb=" N THR A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 484 removed outlier: 3.550A pdb=" N VAL A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 490 through 514 removed outlier: 3.919A pdb=" N ALA A 514 " --> pdb=" O MET A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 544 Processing helix chain 'C' and resid 141 through 147 Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.570A pdb=" N GLN D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLY D 85 " --> pdb=" O LYS D 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 81 through 85' Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.876A pdb=" N THR D 110 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 removed outlier: 3.653A pdb=" N GLY D 182 " --> pdb=" O TRP D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 213 Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 25 removed outlier: 3.683A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.697A pdb=" N MET C 31 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 68 " --> pdb=" O TRP C 55 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN C 57 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU C 66 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 137 through 138 removed outlier: 3.567A pdb=" N VAL C 153 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER C 151 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU C 201 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL C 153 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU C 199 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N PHE C 155 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER C 197 " --> pdb=" O PHE C 155 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN C 157 " --> pdb=" O MET C 195 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N MET C 195 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 170 removed outlier: 3.512A pdb=" N CYS C 214 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 225 " --> pdb=" O ALA C 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 22 through 25 removed outlier: 3.812A pdb=" N VAL D 37 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 102 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.636A pdb=" N MET D 53 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 145 through 146 removed outlier: 4.951A pdb=" N GLY D 164 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL D 206 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU D 166 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N SER D 204 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS D 168 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU D 202 " --> pdb=" O LYS D 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 145 through 146 removed outlier: 4.951A pdb=" N GLY D 164 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL D 206 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU D 166 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N SER D 204 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS D 168 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU D 202 " --> pdb=" O LYS D 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 219 through 222 414 hydrogen bonds defined for protein. 1165 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: 1.93 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1254 1.33 - 1.45: 1461 1.45 - 1.57: 3512 1.57 - 1.69: 0 1.69 - 1.82: 55 Bond restraints: 6282 Sorted by residual: bond pdb=" C LEU A 213 " pdb=" O LEU A 213 " ideal model delta sigma weight residual 1.236 1.303 -0.066 1.15e-02 7.56e+03 3.34e+01 bond pdb=" C ALA A 379 " pdb=" O ALA A 379 " ideal model delta sigma weight residual 1.236 1.298 -0.061 1.15e-02 7.56e+03 2.85e+01 bond pdb=" C SER A 382 " pdb=" O SER A 382 " ideal model delta sigma weight residual 1.236 1.297 -0.061 1.15e-02 7.56e+03 2.78e+01 bond pdb=" C ASP A 166 " pdb=" O ASP A 166 " ideal model delta sigma weight residual 1.235 1.294 -0.058 1.22e-02 6.72e+03 2.28e+01 bond pdb=" C CYS A 217 " pdb=" O CYS A 217 " ideal model delta sigma weight residual 1.236 1.289 -0.053 1.15e-02 7.56e+03 2.14e+01 ... (remaining 6277 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.05: 103 106.05 - 113.09: 3443 113.09 - 120.12: 2262 120.12 - 127.16: 2709 127.16 - 134.19: 52 Bond angle restraints: 8569 Sorted by residual: angle pdb=" N PRO A 397 " pdb=" CA PRO A 397 " pdb=" C PRO A 397 " ideal model delta sigma weight residual 113.47 101.19 12.28 1.43e+00 4.89e-01 7.37e+01 angle pdb=" N PRO D 192 " pdb=" CA PRO D 192 " pdb=" CB PRO D 192 " ideal model delta sigma weight residual 103.31 110.26 -6.95 8.90e-01 1.26e+00 6.11e+01 angle pdb=" N PRO D 148 " pdb=" CA PRO D 148 " pdb=" CB PRO D 148 " ideal model delta sigma weight residual 103.25 111.41 -8.16 1.05e+00 9.07e-01 6.04e+01 angle pdb=" N PRO D 174 " pdb=" CA PRO D 174 " pdb=" CB PRO D 174 " ideal model delta sigma weight residual 103.25 111.13 -7.88 1.05e+00 9.07e-01 5.64e+01 angle pdb=" N PRO D 151 " pdb=" CA PRO D 151 " pdb=" CB PRO D 151 " ideal model delta sigma weight residual 103.25 110.81 -7.56 1.05e+00 9.07e-01 5.19e+01 ... (remaining 8564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 3291 17.11 - 34.22: 269 34.22 - 51.33: 73 51.33 - 68.44: 19 68.44 - 85.55: 5 Dihedral angle restraints: 3657 sinusoidal: 1157 harmonic: 2500 Sorted by residual: dihedral pdb=" CB CYS A 367 " pdb=" SG CYS A 367 " pdb=" SG CYS A 553 " pdb=" CB CYS A 553 " ideal model delta sinusoidal sigma weight residual 93.00 148.53 -55.53 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CA ASP C 102 " pdb=" CB ASP C 102 " pdb=" CG ASP C 102 " pdb=" OD1 ASP C 102 " ideal model delta sinusoidal sigma weight residual -30.00 -89.93 59.93 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA GLU D 108 " pdb=" C GLU D 108 " pdb=" N ASP D 109 " pdb=" CA ASP D 109 " ideal model delta harmonic sigma weight residual -180.00 -164.09 -15.91 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 3654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 652 0.047 - 0.093: 209 0.093 - 0.139: 123 0.139 - 0.185: 27 0.185 - 0.232: 14 Chirality restraints: 1025 Sorted by residual: chirality pdb=" CA PRO D 225 " pdb=" N PRO D 225 " pdb=" C PRO D 225 " pdb=" CB PRO D 225 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA VAL A 192 " pdb=" N VAL A 192 " pdb=" C VAL A 192 " pdb=" CB VAL A 192 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE A 385 " pdb=" CA ILE A 385 " pdb=" CG1 ILE A 385 " pdb=" CG2 ILE A 385 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1022 not shown) Planarity restraints: 1088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 86 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.19e+00 pdb=" C ASN A 86 " -0.050 2.00e-02 2.50e+03 pdb=" O ASN A 86 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 87 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 165 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" C GLU A 165 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU A 165 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP A 166 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 515 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C PRO A 515 " 0.039 2.00e-02 2.50e+03 pdb=" O PRO A 515 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN A 516 " -0.013 2.00e-02 2.50e+03 ... (remaining 1085 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 232 2.71 - 3.26: 6318 3.26 - 3.81: 9660 3.81 - 4.35: 10689 4.35 - 4.90: 19124 Nonbonded interactions: 46023 Sorted by model distance: nonbonded pdb=" N GLU C 101 " pdb=" OE1 GLU C 101 " model vdw 2.169 2.520 nonbonded pdb=" N ALA C 131 " pdb=" CB TYR C 160 " model vdw 2.175 3.520 nonbonded pdb=" OD1 ASN A 100 " pdb="CA CA A 601 " model vdw 2.220 2.510 nonbonded pdb=" O SER D 26 " pdb=" OG1 THR D 133 " model vdw 2.265 2.440 nonbonded pdb=" OE1 GLU A 165 " pdb=" OH TYR D 51 " model vdw 2.311 2.440 ... (remaining 46018 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=0.29 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: 0.530 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: 1.990 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.890 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:14.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 6282 Z= 0.523 Angle : 1.089 12.276 8569 Z= 0.788 Chirality : 0.063 0.232 1025 Planarity : 0.004 0.042 1088 Dihedral : 14.534 85.547 2050 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.93 % Allowed : 6.94 % Favored : 92.13 % Rotamer: Outliers : 3.22 % Allowed : 20.93 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.55 (0.28), residues: 867 helix: 0.61 (0.25), residues: 393 sheet: -0.13 (0.39), residues: 185 loop : -1.81 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 127 HIS 0.004 0.001 HIS A 535 PHE 0.014 0.002 PHE C 91 TYR 0.012 0.001 TYR D 51 ARG 0.005 0.001 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 40 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9258 (mm) REVERT: A 112 MET cc_start: 0.8870 (ttt) cc_final: 0.8639 (tmm) outliers start: 18 outliers final: 5 residues processed: 54 average time/residue: 1.1190 time to fit residues: 64.1692 Evaluate side-chains 40 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 78 optimal weight: 0.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6282 Z= 0.253 Angle : 0.632 8.349 8569 Z= 0.332 Chirality : 0.043 0.146 1025 Planarity : 0.004 0.056 1088 Dihedral : 5.480 59.027 934 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.32 % Favored : 94.21 % Rotamer: Outliers : 3.40 % Allowed : 22.00 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.88 (0.29), residues: 867 helix: 2.28 (0.25), residues: 388 sheet: 0.50 (0.40), residues: 179 loop : -1.73 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 127 HIS 0.003 0.001 HIS A 125 PHE 0.012 0.001 PHE C 91 TYR 0.011 0.001 TYR A 538 ARG 0.003 0.001 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 35 time to evaluate : 0.747 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 49 average time/residue: 1.0082 time to fit residues: 52.8452 Evaluate side-chains 37 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 84 optimal weight: 30.0000 chunk 69 optimal weight: 0.3980 chunk 77 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6282 Z= 0.278 Angle : 0.609 8.630 8569 Z= 0.322 Chirality : 0.042 0.156 1025 Planarity : 0.004 0.048 1088 Dihedral : 5.192 58.871 933 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.13 % Favored : 93.52 % Rotamer: Outliers : 3.58 % Allowed : 22.54 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.31 (0.30), residues: 867 helix: 2.74 (0.25), residues: 387 sheet: 0.55 (0.40), residues: 185 loop : -1.59 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 127 HIS 0.003 0.001 HIS A 535 PHE 0.009 0.001 PHE C 91 TYR 0.009 0.001 TYR A 538 ARG 0.002 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 35 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 132 CYS cc_start: 0.9108 (m) cc_final: 0.8859 (m) REVERT: D 29 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7715 (mm-30) outliers start: 20 outliers final: 7 residues processed: 49 average time/residue: 1.2602 time to fit residues: 65.2180 Evaluate side-chains 41 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 498 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 40.0000 chunk 58 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 50.0000 chunk 83 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN C 57 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 6282 Z= 0.431 Angle : 0.689 8.834 8569 Z= 0.368 Chirality : 0.044 0.174 1025 Planarity : 0.005 0.047 1088 Dihedral : 5.224 58.036 932 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.83 % Favored : 92.82 % Rotamer: Outliers : 3.04 % Allowed : 23.97 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.28 (0.29), residues: 867 helix: 2.54 (0.25), residues: 387 sheet: 0.65 (0.39), residues: 183 loop : -1.41 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 127 HIS 0.004 0.001 HIS A 32 PHE 0.010 0.001 PHE C 91 TYR 0.019 0.001 TYR A 501 ARG 0.003 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 36 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 132 CYS cc_start: 0.9142 (m) cc_final: 0.8856 (m) REVERT: D 29 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7785 (mm-30) outliers start: 17 outliers final: 7 residues processed: 51 average time/residue: 1.1636 time to fit residues: 62.9122 Evaluate side-chains 40 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 37 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN D 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6282 Z= 0.224 Angle : 0.584 8.116 8569 Z= 0.305 Chirality : 0.041 0.155 1025 Planarity : 0.004 0.049 1088 Dihedral : 4.981 59.954 932 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.90 % Favored : 93.75 % Rotamer: Outliers : 3.04 % Allowed : 24.33 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.58 (0.30), residues: 867 helix: 2.85 (0.25), residues: 388 sheet: 0.79 (0.40), residues: 180 loop : -1.35 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 82 HIS 0.002 0.001 HIS A 535 PHE 0.010 0.001 PHE A 360 TYR 0.011 0.001 TYR A 501 ARG 0.002 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 36 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 CYS cc_start: 0.9165 (m) cc_final: 0.8899 (m) REVERT: C 51 THR cc_start: 0.9505 (OUTLIER) cc_final: 0.9272 (m) REVERT: D 29 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7671 (mm-30) outliers start: 17 outliers final: 7 residues processed: 51 average time/residue: 1.1988 time to fit residues: 64.8587 Evaluate side-chains 43 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 51 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 50.0000 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6282 Z= 0.262 Angle : 0.620 9.207 8569 Z= 0.318 Chirality : 0.042 0.154 1025 Planarity : 0.004 0.048 1088 Dihedral : 4.674 59.327 930 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.13 % Favored : 93.52 % Rotamer: Outliers : 2.33 % Allowed : 25.04 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.64 (0.30), residues: 867 helix: 2.82 (0.25), residues: 390 sheet: 0.81 (0.40), residues: 186 loop : -1.25 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 127 HIS 0.002 0.001 HIS A 32 PHE 0.009 0.001 PHE A 360 TYR 0.015 0.001 TYR A 501 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 36 time to evaluate : 0.727 Fit side-chains REVERT: A 132 CYS cc_start: 0.9167 (m) cc_final: 0.8895 (m) REVERT: C 51 THR cc_start: 0.9498 (OUTLIER) cc_final: 0.9263 (m) REVERT: D 29 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7764 (mm-30) outliers start: 13 outliers final: 6 residues processed: 46 average time/residue: 1.2145 time to fit residues: 59.6573 Evaluate side-chains 42 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 51 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 50.0000 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 82 optimal weight: 40.0000 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN D 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6282 Z= 0.164 Angle : 0.594 10.402 8569 Z= 0.299 Chirality : 0.041 0.162 1025 Planarity : 0.004 0.053 1088 Dihedral : 4.089 48.495 927 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.21 % Favored : 94.44 % Rotamer: Outliers : 2.33 % Allowed : 25.04 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.91 (0.30), residues: 867 helix: 3.04 (0.26), residues: 388 sheet: 1.00 (0.40), residues: 187 loop : -1.13 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 69 HIS 0.002 0.001 HIS A 535 PHE 0.010 0.001 PHE A 360 TYR 0.011 0.001 TYR A 501 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 CYS cc_start: 0.9183 (m) cc_final: 0.8830 (m) REVERT: D 29 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7822 (mm-30) outliers start: 13 outliers final: 6 residues processed: 55 average time/residue: 1.1547 time to fit residues: 67.4001 Evaluate side-chains 45 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 553 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 56 optimal weight: 0.0060 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 50.0000 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6282 Z= 0.175 Angle : 0.599 11.370 8569 Z= 0.301 Chirality : 0.041 0.151 1025 Planarity : 0.004 0.056 1088 Dihedral : 4.030 47.462 927 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.44 % Favored : 94.21 % Rotamer: Outliers : 1.97 % Allowed : 25.04 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.00 (0.30), residues: 867 helix: 3.11 (0.26), residues: 388 sheet: 1.14 (0.41), residues: 181 loop : -1.10 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.002 0.000 HIS A 535 PHE 0.010 0.001 PHE A 360 TYR 0.011 0.001 TYR A 501 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8771 (mtp) cc_final: 0.8479 (mpp) REVERT: A 132 CYS cc_start: 0.9212 (m) cc_final: 0.8935 (m) REVERT: D 29 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7798 (mm-30) outliers start: 11 outliers final: 6 residues processed: 51 average time/residue: 1.1303 time to fit residues: 61.2651 Evaluate side-chains 46 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 553 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 60 optimal weight: 40.0000 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 81 optimal weight: 40.0000 chunk 49 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN D 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 6282 Z= 0.534 Angle : 0.774 11.822 8569 Z= 0.403 Chirality : 0.045 0.159 1025 Planarity : 0.005 0.054 1088 Dihedral : 4.477 48.348 927 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.37 % Favored : 93.29 % Rotamer: Outliers : 1.79 % Allowed : 25.76 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.50 (0.29), residues: 867 helix: 2.41 (0.25), residues: 393 sheet: 0.97 (0.39), residues: 189 loop : -1.08 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 224 HIS 0.004 0.001 HIS A 32 PHE 0.009 0.002 PHE C 107 TYR 0.025 0.002 TYR A 501 ARG 0.004 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.748 Fit side-chains REVERT: D 29 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7817 (mm-30) REVERT: D 65 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8050 (mp0) outliers start: 10 outliers final: 4 residues processed: 45 average time/residue: 1.3501 time to fit residues: 64.0032 Evaluate side-chains 40 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 507 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 85 optimal weight: 50.0000 chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6282 Z= 0.204 Angle : 0.664 12.718 8569 Z= 0.336 Chirality : 0.042 0.184 1025 Planarity : 0.004 0.051 1088 Dihedral : 4.221 46.556 927 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.09 % Favored : 94.56 % Rotamer: Outliers : 1.43 % Allowed : 25.94 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.30), residues: 867 helix: 2.85 (0.25), residues: 390 sheet: 1.10 (0.41), residues: 181 loop : -1.06 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 69 HIS 0.002 0.000 HIS A 535 PHE 0.010 0.001 PHE A 360 TYR 0.015 0.001 TYR A 501 ARG 0.001 0.000 ARG A 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.687 Fit side-chains REVERT: A 123 MET cc_start: 0.8737 (mtp) cc_final: 0.8469 (mpp) REVERT: D 29 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7689 (mm-30) outliers start: 8 outliers final: 4 residues processed: 45 average time/residue: 1.3191 time to fit residues: 62.7106 Evaluate side-chains 41 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 507 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 50.0000 chunk 10 optimal weight: 0.0570 chunk 18 optimal weight: 0.0000 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 50.0000 chunk 3 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.068771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.050566 restraints weight = 72282.489| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 5.99 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6282 Z= 0.187 Angle : 0.653 12.905 8569 Z= 0.327 Chirality : 0.041 0.197 1025 Planarity : 0.004 0.058 1088 Dihedral : 4.052 45.895 927 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.56 % Favored : 94.10 % Rotamer: Outliers : 1.61 % Allowed : 25.40 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.03 (0.30), residues: 867 helix: 3.01 (0.26), residues: 388 sheet: 1.22 (0.41), residues: 181 loop : -0.93 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.002 0.001 HIS A 535 PHE 0.010 0.001 PHE A 360 TYR 0.010 0.001 TYR A 501 ARG 0.003 0.000 ARG A 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1866.76 seconds wall clock time: 34 minutes 4.45 seconds (2044.45 seconds total)