Starting phenix.real_space_refine on Fri Dec 8 13:33:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsl_18635/12_2023/8qsl_18635_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsl_18635/12_2023/8qsl_18635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsl_18635/12_2023/8qsl_18635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsl_18635/12_2023/8qsl_18635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsl_18635/12_2023/8qsl_18635_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsl_18635/12_2023/8qsl_18635_neut.pdb" } resolution = 2.81 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= -0.001 sd= 0.018 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 P 2 5.49 5 S 48 5.16 5 C 5702 2.51 5 N 1310 2.21 5 O 1444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 44": "OE1" <-> "OE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ASP 558": "OD1" <-> "OD2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ASP 558": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8506 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 23, 'TRANS': 499} Chain breaks: 1 Chain: "C" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 23, 'TRANS': 499} Chain breaks: 1 Chain: "A" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'NAG': 1, 'PGT': 1, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 275 Unusual residues: {'NAG': 1, 'PGT': 1, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.44, per 1000 atoms: 0.64 Number of scatterers: 8506 At special positions: 0 Unit cell: (122.265, 80.465, 87.78, 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) S 48 16.00 P 2 15.00 O 1444 8.00 N 1310 7.00 C 5702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 153 " 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=2, symmetry=0 Links applied NAG-ASN " NAG A 604 " - " ASN A 140 " " NAG C 604 " - " ASN C 140 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.7 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 81.8% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 removed outlier: 3.834A pdb=" N ALA A 20 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 57 removed outlier: 3.797A pdb=" N CYS A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 70 through 98 removed outlier: 3.981A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 101 through 118 Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.887A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 153 through 183 removed outlier: 4.402A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.874A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 220 removed outlier: 3.796A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 248 removed outlier: 3.610A pdb=" N ALA A 227 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 4.166A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 removed outlier: 3.972A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A 265 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 4.059A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 347 removed outlier: 3.671A pdb=" N VAL A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix removed outlier: 4.014A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 367 through 395 removed outlier: 4.880A pdb=" N ASP A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Proline residue: A 382 - end of helix removed outlier: 4.648A pdb=" N ASP A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix removed outlier: 3.917A pdb=" N HIS A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 431 removed outlier: 3.789A pdb=" N ARG A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 480 removed outlier: 4.596A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 511 Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 531 through 560 removed outlier: 4.049A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 29 removed outlier: 4.071A pdb=" N ALA C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 57 removed outlier: 3.771A pdb=" N CYS C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 70 through 98 removed outlier: 3.987A pdb=" N SER C 89 " --> pdb=" O THR C 85 " (cutoff:3.500A) Proline residue: C 90 - end of helix Processing helix chain 'C' and resid 101 through 125 removed outlier: 4.200A pdb=" N ALA C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) Proline residue: C 121 - end of helix Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 153 through 183 removed outlier: 4.360A pdb=" N THR C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) Proline residue: C 177 - end of helix removed outlier: 3.873A pdb=" N VAL C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 220 removed outlier: 3.797A pdb=" N ALA C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 248 removed outlier: 3.630A pdb=" N ALA C 227 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C 228 " --> pdb=" O THR C 224 " (cutoff:3.500A) Proline residue: C 229 - end of helix removed outlier: 4.164A pdb=" N SER C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL C 246 " --> pdb=" O CYS C 242 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 273 removed outlier: 3.893A pdb=" N MET C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 265 " --> pdb=" O PHE C 261 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 removed outlier: 4.060A pdb=" N GLY C 304 " --> pdb=" O LYS C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 347 removed outlier: 3.705A pdb=" N VAL C 312 " --> pdb=" O THR C 308 " (cutoff:3.500A) Proline residue: C 323 - end of helix Proline residue: C 330 - end of helix removed outlier: 4.012A pdb=" N VAL C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 367 through 395 removed outlier: 4.824A pdb=" N ASP C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA C 374 " --> pdb=" O THR C 370 " (cutoff:3.500A) Proline residue: C 382 - end of helix removed outlier: 4.653A pdb=" N ASP C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Proline residue: C 390 - end of helix removed outlier: 3.918A pdb=" N HIS C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 431 removed outlier: 3.821A pdb=" N ARG C 404 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 453 Processing helix chain 'C' and resid 454 through 480 removed outlier: 4.608A pdb=" N ILE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 480 " --> pdb=" O ALA C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 511 Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 531 through 560 removed outlier: 4.084A pdb=" N TYR C 535 " --> pdb=" O TYR C 531 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AA2, first strand: chain 'C' and resid 435 through 436 594 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1316 1.32 - 1.44: 2295 1.44 - 1.57: 5057 1.57 - 1.69: 4 1.69 - 1.81: 70 Bond restraints: 8742 Sorted by residual: bond pdb=" N GLY A 16 " pdb=" CA GLY A 16 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.36e+00 bond pdb=" N GLY C 16 " pdb=" CA GLY C 16 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.13e+00 bond pdb=" CB GLN C 182 " pdb=" CG GLN C 182 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.00e+00 bond pdb=" CB GLN A 182 " pdb=" CG GLN A 182 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.74e-01 bond pdb=" CB LYS A 513 " pdb=" CG LYS A 513 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.26e-01 ... (remaining 8737 not shown) Histogram of bond angle deviations from ideal: 93.41 - 101.52: 30 101.52 - 109.63: 890 109.63 - 117.74: 5902 117.74 - 125.85: 4962 125.85 - 133.97: 148 Bond angle restraints: 11932 Sorted by residual: angle pdb=" N SER A 255 " pdb=" CA SER A 255 " pdb=" C SER A 255 " ideal model delta sigma weight residual 113.43 108.80 4.63 1.26e+00 6.30e-01 1.35e+01 angle pdb=" N SER C 255 " pdb=" CA SER C 255 " pdb=" C SER C 255 " ideal model delta sigma weight residual 113.43 109.15 4.28 1.26e+00 6.30e-01 1.15e+01 angle pdb=" C VAL A 322 " pdb=" CA VAL A 322 " pdb=" CB VAL A 322 " ideal model delta sigma weight residual 113.70 110.57 3.13 9.50e-01 1.11e+00 1.08e+01 angle pdb=" OG1 THR C 359 " pdb=" CB THR C 359 " pdb=" CG2 THR C 359 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.93e+00 angle pdb=" OG1 THR C 358 " pdb=" CB THR C 358 " pdb=" CG2 THR C 358 " ideal model delta sigma weight residual 109.30 103.33 5.97 2.00e+00 2.50e-01 8.90e+00 ... (remaining 11927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.78: 5472 30.78 - 61.56: 246 61.56 - 92.34: 14 92.34 - 123.12: 0 123.12 - 153.90: 2 Dihedral angle restraints: 5734 sinusoidal: 2742 harmonic: 2992 Sorted by residual: dihedral pdb=" CA GLY C 396 " pdb=" C GLY C 396 " pdb=" N LEU C 397 " pdb=" CA LEU C 397 " ideal model delta harmonic sigma weight residual -180.00 -157.22 -22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLY A 396 " pdb=" C GLY A 396 " pdb=" N LEU A 397 " pdb=" CA LEU A 397 " ideal model delta harmonic sigma weight residual -180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" C3 PGT A 608 " pdb=" C1 PGT A 608 " pdb=" C2 PGT A 608 " pdb=" O3P PGT A 608 " ideal model delta sinusoidal sigma weight residual -66.13 87.77 -153.90 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 5731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1029 0.034 - 0.067: 260 0.067 - 0.101: 88 0.101 - 0.135: 15 0.135 - 0.169: 6 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CB THR C 358 " pdb=" CA THR C 358 " pdb=" OG1 THR C 358 " pdb=" CG2 THR C 358 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CB THR C 359 " pdb=" CA THR C 359 " pdb=" OG1 THR C 359 " pdb=" CG2 THR C 359 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CB THR A 359 " pdb=" CA THR A 359 " pdb=" OG1 THR A 359 " pdb=" CG2 THR A 359 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 1395 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 452 " 0.019 2.00e-02 2.50e+03 1.49e-02 5.57e+00 pdb=" CG TRP C 452 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 452 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 452 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 452 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 452 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 452 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 452 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 452 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 452 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 452 " 0.017 2.00e-02 2.50e+03 1.31e-02 4.30e+00 pdb=" CG TRP A 452 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 452 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 452 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 452 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 452 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 452 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 452 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 452 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 452 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 356 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C ASN A 356 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN A 356 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 357 " 0.010 2.00e-02 2.50e+03 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 96 2.55 - 3.14: 7830 3.14 - 3.73: 13398 3.73 - 4.31: 17834 4.31 - 4.90: 29454 Nonbonded interactions: 68612 Sorted by model distance: nonbonded pdb=" O ALA A 227 " pdb=" OG1 THR A 230 " model vdw 1.968 2.440 nonbonded pdb=" O ALA C 227 " pdb=" OG1 THR C 230 " model vdw 1.973 2.440 nonbonded pdb=" O GLN C 218 " pdb=" NE2 GLN C 218 " model vdw 2.037 2.520 nonbonded pdb=" OG SER A 346 " pdb=" OE1 GLN A 454 " model vdw 2.063 2.440 nonbonded pdb=" OG SER C 346 " pdb=" OE1 GLN C 454 " model vdw 2.067 2.440 ... (remaining 68607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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: 0.630 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: 3.330 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 27.090 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.004 0.040 8742 Z= 0.236 Angle : 0.671 8.420 11932 Z= 0.350 Chirality : 0.036 0.169 1398 Planarity : 0.004 0.032 1410 Dihedral : 15.580 153.903 3806 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.12 % Allowed : 25.85 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.27), residues: 1038 helix: 2.28 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -2.92 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 452 HIS 0.004 0.001 HIS C 348 PHE 0.017 0.001 PHE A 194 TYR 0.006 0.001 TYR C 86 ARG 0.002 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.7204 time to fit residues: 151.1934 Evaluate side-chains 156 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 356 ASN C 218 GLN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8742 Z= 0.239 Angle : 0.752 8.135 11932 Z= 0.359 Chirality : 0.041 0.214 1398 Planarity : 0.005 0.040 1410 Dihedral : 11.471 149.516 2106 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.29 % Allowed : 24.27 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 1038 helix: 2.18 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -2.55 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 452 HIS 0.003 0.001 HIS C 348 PHE 0.023 0.002 PHE A 194 TYR 0.013 0.001 TYR C 226 ARG 0.004 0.001 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 184 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 7 residues processed: 191 average time/residue: 0.7248 time to fit residues: 153.3672 Evaluate side-chains 162 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.5535 time to fit residues: 3.0568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 75 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 218 GLN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN C 218 GLN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8742 Z= 0.272 Angle : 0.791 9.604 11932 Z= 0.368 Chirality : 0.043 0.401 1398 Planarity : 0.005 0.061 1410 Dihedral : 11.422 146.516 2106 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.88 % Allowed : 24.63 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.27), residues: 1038 helix: 2.13 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -2.69 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 452 HIS 0.002 0.001 HIS A 348 PHE 0.019 0.002 PHE A 550 TYR 0.018 0.001 TYR A 226 ARG 0.003 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 173 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 13 residues processed: 191 average time/residue: 0.6386 time to fit residues: 136.7442 Evaluate side-chains 164 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 6 residues processed: 7 average time/residue: 0.5470 time to fit residues: 5.5062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 345 GLN A 356 ASN A 457 GLN C 218 GLN ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 8742 Z= 0.233 Angle : 0.780 10.945 11932 Z= 0.360 Chirality : 0.044 0.368 1398 Planarity : 0.004 0.051 1410 Dihedral : 11.257 144.285 2106 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 6.71 % Allowed : 23.54 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.28), residues: 1038 helix: 2.03 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -2.78 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 452 HIS 0.002 0.001 HIS C 395 PHE 0.021 0.002 PHE A 325 TYR 0.022 0.001 TYR C 226 ARG 0.002 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 172 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 21 residues processed: 209 average time/residue: 0.6525 time to fit residues: 152.2524 Evaluate side-chains 170 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 7 average time/residue: 0.5476 time to fit residues: 5.4324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 356 ASN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8742 Z= 0.228 Angle : 0.831 11.596 11932 Z= 0.374 Chirality : 0.046 0.377 1398 Planarity : 0.004 0.049 1410 Dihedral : 11.130 142.941 2106 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.37 % Allowed : 26.10 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.28), residues: 1038 helix: 1.93 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -2.73 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 452 HIS 0.002 0.001 HIS C 560 PHE 0.036 0.002 PHE C 550 TYR 0.018 0.001 TYR A 226 ARG 0.005 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 168 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 21 residues processed: 198 average time/residue: 0.6969 time to fit residues: 153.4314 Evaluate side-chains 163 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 142 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 16 residues processed: 5 average time/residue: 0.7873 time to fit residues: 5.4939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8742 Z= 0.246 Angle : 0.847 12.342 11932 Z= 0.381 Chirality : 0.050 0.576 1398 Planarity : 0.004 0.046 1410 Dihedral : 11.194 141.756 2106 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.23 % Favored : 92.58 % Rotamer: Outliers : 4.27 % Allowed : 28.54 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.28), residues: 1038 helix: 1.90 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -2.84 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 452 HIS 0.001 0.001 HIS C 348 PHE 0.022 0.001 PHE C 536 TYR 0.014 0.001 TYR A 226 ARG 0.002 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 186 average time/residue: 0.6930 time to fit residues: 143.4459 Evaluate side-chains 168 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 1.8359 time to fit residues: 5.0662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 0.0570 chunk 56 optimal weight: 0.5980 chunk 84 optimal weight: 0.1980 chunk 100 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8742 Z= 0.214 Angle : 0.829 12.937 11932 Z= 0.370 Chirality : 0.047 0.384 1398 Planarity : 0.004 0.047 1410 Dihedral : 11.109 140.446 2106 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.03 % Favored : 92.77 % Rotamer: Outliers : 4.76 % Allowed : 28.90 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.28), residues: 1038 helix: 1.90 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -2.73 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 453 HIS 0.002 0.000 HIS A 560 PHE 0.023 0.001 PHE C 536 TYR 0.013 0.001 TYR A 226 ARG 0.002 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 163 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 29 residues processed: 190 average time/residue: 0.6759 time to fit residues: 143.0493 Evaluate side-chains 170 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 0.839 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 6 average time/residue: 0.8486 time to fit residues: 6.7612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 87 optimal weight: 0.0020 chunk 93 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8742 Z= 0.224 Angle : 0.851 13.377 11932 Z= 0.381 Chirality : 0.046 0.394 1398 Planarity : 0.004 0.049 1410 Dihedral : 10.985 139.284 2106 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.84 % Favored : 92.97 % Rotamer: Outliers : 4.15 % Allowed : 30.98 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.28), residues: 1038 helix: 1.86 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -2.68 (0.44), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 368 HIS 0.001 0.000 HIS C 521 PHE 0.018 0.001 PHE C 536 TYR 0.019 0.001 TYR A 226 ARG 0.001 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 24 residues processed: 182 average time/residue: 0.6942 time to fit residues: 140.3861 Evaluate side-chains 168 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 3 average time/residue: 1.0221 time to fit residues: 4.3678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 40 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8742 Z= 0.217 Angle : 0.861 13.888 11932 Z= 0.385 Chirality : 0.046 0.401 1398 Planarity : 0.004 0.047 1410 Dihedral : 10.821 138.011 2106 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.02 % Allowed : 31.46 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 1038 helix: 1.88 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -2.73 (0.43), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 452 HIS 0.002 0.000 HIS C 303 PHE 0.030 0.001 PHE C 307 TYR 0.020 0.001 TYR C 226 ARG 0.001 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 0.966 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 192 average time/residue: 0.6770 time to fit residues: 144.7789 Evaluate side-chains 170 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 1.5830 time to fit residues: 2.9247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8742 Z= 0.238 Angle : 0.890 13.982 11932 Z= 0.400 Chirality : 0.047 0.409 1398 Planarity : 0.004 0.056 1410 Dihedral : 10.667 137.000 2106 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.05 % Allowed : 33.90 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.28), residues: 1038 helix: 1.84 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -2.79 (0.44), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 452 HIS 0.003 0.001 HIS A 303 PHE 0.027 0.002 PHE C 307 TYR 0.039 0.001 TYR C 226 ARG 0.002 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 0.909 Fit side-chains outliers start: 25 outliers final: 19 residues processed: 180 average time/residue: 0.6915 time to fit residues: 138.2813 Evaluate side-chains 162 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 1.4578 time to fit residues: 2.7336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 84 optimal weight: 0.0670 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.138642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.110295 restraints weight = 16950.840| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.40 r_work: 0.3645 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8742 Z= 0.233 Angle : 0.890 14.003 11932 Z= 0.405 Chirality : 0.048 0.408 1398 Planarity : 0.004 0.054 1410 Dihedral : 10.544 135.916 2106 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.68 % Allowed : 35.12 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.28), residues: 1038 helix: 1.81 (0.18), residues: 782 sheet: None (None), residues: 0 loop : -2.88 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 452 HIS 0.001 0.001 HIS C 560 PHE 0.036 0.002 PHE C 61 TYR 0.057 0.001 TYR C 226 ARG 0.001 0.000 ARG C 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2915.94 seconds wall clock time: 52 minutes 49.59 seconds (3169.59 seconds total)