Starting phenix.real_space_refine on Wed Feb 12 12:43:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sni_10258/02_2025/6sni_10258.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sni_10258/02_2025/6sni_10258.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/cci-nas-00/data/ceres_data/6sni_10258/02_2025/6sni_10258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sni_10258/02_2025/6sni_10258.map" model { file = "/net/cci-nas-00/data/ceres_data/6sni_10258/02_2025/6sni_10258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sni_10258/02_2025/6sni_10258.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 1 5.49 5 S 31 5.16 5 C 4967 2.51 5 N 1156 2.21 5 O 1355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7510 Number of models: 1 Model: "" Number of chains: 7 Chain: "X" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3924 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 25, 'TRANS': 453} Chain breaks: 1 Chain: "H" Number of atoms: 1687 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} Conformer: "B" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} bond proxies already assigned to first conformer: 1725 Chain: "L" Number of atoms: 1659 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1654 Chain: "X" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 163 Unusual residues: {'PTY': 5, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 3} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.56, per 1000 atoms: 0.87 Number of scatterers: 7510 At special positions: 0 Unit cell: (115.92, 86.52, 113.4, 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 31 16.00 P 1 15.00 O 1355 8.00 N 1156 7.00 C 4967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS X 314 " - pdb=" SG CYS X 515 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.2 seconds 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 42.7% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'X' and resid 41 through 53 removed outlier: 3.886A pdb=" N VAL X 47 " --> pdb=" O PHE X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 56 No H-bonds generated for 'chain 'X' and resid 54 through 56' Processing helix chain 'X' and resid 68 through 81 removed outlier: 3.749A pdb=" N ALA X 72 " --> pdb=" O GLY X 68 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN X 73 " --> pdb=" O ASP X 69 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN X 81 " --> pdb=" O MET X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 119 removed outlier: 3.674A pdb=" N ALA X 105 " --> pdb=" O PRO X 101 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE X 118 " --> pdb=" O ILE X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 154 removed outlier: 3.541A pdb=" N ILE X 147 " --> pdb=" O ARG X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 170 Processing helix chain 'X' and resid 172 through 185 removed outlier: 3.593A pdb=" N ALA X 179 " --> pdb=" O GLY X 175 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE X 183 " --> pdb=" O ALA X 179 " (cutoff:3.500A) Processing helix chain 'X' and resid 186 through 194 Processing helix chain 'X' and resid 199 through 217 removed outlier: 4.425A pdb=" N MET X 203 " --> pdb=" O TYR X 199 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR X 207 " --> pdb=" O MET X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 218 through 231 removed outlier: 3.921A pdb=" N VAL X 224 " --> pdb=" O ALA X 220 " (cutoff:3.500A) Processing helix chain 'X' and resid 232 through 237 removed outlier: 6.959A pdb=" N MET X 235 " --> pdb=" O PHE X 232 " (cutoff:3.500A) Processing helix chain 'X' and resid 239 through 253 removed outlier: 4.127A pdb=" N ALA X 245 " --> pdb=" O PRO X 241 " (cutoff:3.500A) Processing helix chain 'X' and resid 258 through 282 removed outlier: 3.904A pdb=" N LEU X 262 " --> pdb=" O ASN X 258 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU X 270 " --> pdb=" O ALA X 266 " (cutoff:3.500A) Proline residue: X 279 - end of helix Processing helix chain 'X' and resid 286 through 298 removed outlier: 3.596A pdb=" N ILE X 290 " --> pdb=" O GLY X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 317 removed outlier: 3.729A pdb=" N THR X 316 " --> pdb=" O PHE X 312 " (cutoff:3.500A) Processing helix chain 'X' and resid 321 through 325 Processing helix chain 'X' and resid 327 through 352 removed outlier: 3.647A pdb=" N LEU X 336 " --> pdb=" O GLN X 332 " (cutoff:3.500A) Proline residue: X 345 - end of helix Processing helix chain 'X' and resid 358 through 374 removed outlier: 3.666A pdb=" N SER X 369 " --> pdb=" O ALA X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 382 through 392 Proline residue: X 388 - end of helix Processing helix chain 'X' and resid 393 through 395 No H-bonds generated for 'chain 'X' and resid 393 through 395' Processing helix chain 'X' and resid 398 through 414 Processing helix chain 'X' and resid 415 through 421 removed outlier: 3.846A pdb=" N LYS X 421 " --> pdb=" O PRO X 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 424 through 440 removed outlier: 3.508A pdb=" N ALA X 429 " --> pdb=" O HIS X 425 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN X 436 " --> pdb=" O PHE X 432 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY X 440 " --> pdb=" O ASN X 436 " (cutoff:3.500A) Processing helix chain 'X' and resid 476 through 491 removed outlier: 3.845A pdb=" N LYS X 480 " --> pdb=" O ASN X 476 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER X 481 " --> pdb=" O VAL X 477 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE X 482 " --> pdb=" O VAL X 478 " (cutoff:3.500A) Processing helix chain 'X' and resid 492 through 497 removed outlier: 3.623A pdb=" N LEU X 496 " --> pdb=" O PHE X 492 " (cutoff:3.500A) Processing helix chain 'X' and resid 509 through 536 removed outlier: 3.554A pdb=" N GLY X 518 " --> pdb=" O ASN X 514 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE X 519 " --> pdb=" O CYS X 515 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE X 520 " --> pdb=" O ALA X 516 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS X 521 " --> pdb=" O VAL X 517 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU X 527 " --> pdb=" O SER X 523 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE X 534 " --> pdb=" O TYR X 530 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.674A pdb=" N SER H 31 " --> pdb=" O ASN H 28 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 101 through 105 removed outlier: 3.624A pdb=" N SER H 104 " --> pdb=" O SER H 101 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR H 105 " --> pdb=" O TRP H 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 101 through 105' Processing helix chain 'H' and resid 194 through 198 removed outlier: 4.024A pdb=" N LEU H 198 " --> pdb=" O SER H 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.299A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 removed outlier: 3.584A pdb=" N LYS L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 191 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.985A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER H 58 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.912A pdb=" N TYR H 111 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 129 through 133 removed outlier: 6.186A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 160 through 162 removed outlier: 4.386A pdb=" N TYR H 203 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.800A pdb=" N LEU L 11 " --> pdb=" O LYS L 105 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.514A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 89 through 91 Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.898A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 147 through 152 341 hydrogen bonds defined for protein. 947 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: 2.16 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1122 1.30 - 1.44: 2314 1.44 - 1.58: 4221 1.58 - 1.72: 33 1.72 - 1.86: 47 Bond restraints: 7737 Sorted by residual: bond pdb=" CAK Y01 H2202 " pdb=" CBD Y01 H2202 " ideal model delta sigma weight residual 1.525 1.160 0.365 2.00e-02 2.50e+03 3.33e+02 bond pdb=" CAU Y01 H2202 " pdb=" CBI Y01 H2202 " ideal model delta sigma weight residual 1.530 1.166 0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAK Y01 X1606 " pdb=" CBD Y01 X1606 " ideal model delta sigma weight residual 1.525 1.162 0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" CAU Y01 X1606 " pdb=" CBI Y01 X1606 " ideal model delta sigma weight residual 1.530 1.172 0.358 2.00e-02 2.50e+03 3.20e+02 bond pdb=" CAK Y01 H2201 " pdb=" CBD Y01 H2201 " ideal model delta sigma weight residual 1.525 1.168 0.357 2.00e-02 2.50e+03 3.18e+02 ... (remaining 7732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 10323 3.27 - 6.55: 175 6.55 - 9.82: 26 9.82 - 13.09: 5 13.09 - 16.37: 5 Bond angle restraints: 10534 Sorted by residual: angle pdb=" CA PRO H 156 " pdb=" N PRO H 156 " pdb=" CD PRO H 156 " ideal model delta sigma weight residual 111.50 98.22 13.28 1.40e+00 5.10e-01 9.00e+01 angle pdb=" O SER L 10 " pdb=" C SER L 10 " pdb=" CA ASER L 10 " ideal model delta sigma weight residual 119.98 130.90 -10.92 1.22e+00 6.72e-01 8.00e+01 angle pdb=" O SER L 10 " pdb=" C SER L 10 " pdb=" CA BSER L 10 " ideal model delta sigma weight residual 119.98 130.90 -10.92 1.22e+00 6.72e-01 8.00e+01 angle pdb=" N SER L 10 " pdb=" CA ASER L 10 " pdb=" C SER L 10 " ideal model delta sigma weight residual 107.93 121.33 -13.40 1.65e+00 3.67e-01 6.59e+01 angle pdb=" N SER L 10 " pdb=" CA BSER L 10 " pdb=" C SER L 10 " ideal model delta sigma weight residual 107.93 121.33 -13.40 1.65e+00 3.67e-01 6.59e+01 ... (remaining 10529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4250 17.99 - 35.98: 313 35.98 - 53.97: 98 53.97 - 71.96: 22 71.96 - 89.94: 2 Dihedral angle restraints: 4685 sinusoidal: 1966 harmonic: 2719 Sorted by residual: dihedral pdb=" CA MET X 541 " pdb=" C MET X 541 " pdb=" N LYS X 542 " pdb=" CA LYS X 542 " ideal model delta harmonic sigma weight residual -180.00 -153.98 -26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CB CYS X 314 " pdb=" SG CYS X 314 " pdb=" SG CYS X 515 " pdb=" CB CYS X 515 " ideal model delta sinusoidal sigma weight residual -86.00 -126.33 40.33 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA TRP X 90 " pdb=" C TRP X 90 " pdb=" N TYR X 91 " pdb=" CA TYR X 91 " ideal model delta harmonic sigma weight residual 180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 1144 0.315 - 0.631: 12 0.631 - 0.946: 3 0.946 - 1.262: 0 1.262 - 1.577: 3 Chirality restraints: 1162 Sorted by residual: chirality pdb=" CBD Y01 H2201 " pdb=" CAK Y01 H2201 " pdb=" CBF Y01 H2201 " pdb=" CBG Y01 H2201 " both_signs ideal model delta sigma weight residual False 2.70 1.12 1.58 2.00e-01 2.50e+01 6.22e+01 chirality pdb=" CBD Y01 X1606 " pdb=" CAK Y01 X1606 " pdb=" CBF Y01 X1606 " pdb=" CBG Y01 X1606 " both_signs ideal model delta sigma weight residual False 2.70 1.12 1.57 2.00e-01 2.50e+01 6.19e+01 chirality pdb=" CBD Y01 H2202 " pdb=" CAK Y01 H2202 " pdb=" CBF Y01 H2202 " pdb=" CBG Y01 H2202 " both_signs ideal model delta sigma weight residual False 2.70 1.13 1.56 2.00e-01 2.50e+01 6.11e+01 ... (remaining 1159 not shown) Planarity restraints: 1275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA X 278 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO X 279 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO X 279 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO X 279 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 193 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.20e+00 pdb=" N PRO H 194 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO H 194 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 194 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE X 384 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO X 385 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO X 385 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO X 385 " 0.020 5.00e-02 4.00e+02 ... (remaining 1272 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 102 2.62 - 3.19: 6680 3.19 - 3.76: 10613 3.76 - 4.33: 16211 4.33 - 4.90: 27373 Nonbonded interactions: 60979 Sorted by model distance: nonbonded pdb=" O LYS X 380 " pdb=" OG1 THR X 381 " model vdw 2.044 3.040 nonbonded pdb=" CE1 TYR H 154 " pdb=" OE2 GLU H 157 " model vdw 2.057 3.340 nonbonded pdb=" O THR H 140 " pdb=" OG SER H 195 " model vdw 2.201 3.040 nonbonded pdb=" O GLN L 126 " pdb=" OG SER L 129 " model vdw 2.201 3.040 nonbonded pdb=" N GLU H 6 " pdb=" OE1 GLU H 6 " model vdw 2.206 3.120 ... (remaining 60974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.30 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.620 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 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 : 0.020 0.365 7737 Z= 1.341 Angle : 1.038 16.368 10534 Z= 0.549 Chirality : 0.106 1.577 1162 Planarity : 0.004 0.039 1275 Dihedral : 14.298 89.944 2936 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.23 % Favored : 90.55 % Rotamer: Outliers : 8.07 % Allowed : 8.20 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.23), residues: 917 helix: -2.35 (0.22), residues: 343 sheet: -1.68 (0.35), residues: 193 loop : -3.79 (0.25), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 90 HIS 0.008 0.001 HIS H 35 PHE 0.019 0.001 PHE X 197 TYR 0.016 0.002 TYR L 175 ARG 0.003 0.001 ARG L 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 111 time to evaluate : 0.796 Fit side-chains REVERT: X 98 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8135 (tt) REVERT: X 142 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7852 (mmt) REVERT: X 167 ARG cc_start: 0.7684 (tmm160) cc_final: 0.6745 (mtm110) REVERT: X 473 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8018 (mt) REVERT: H 46 GLU cc_start: 0.7778 (tt0) cc_final: 0.7541 (tt0) REVERT: H 157 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5519 (mp0) outliers start: 65 outliers final: 33 residues processed: 167 average time/residue: 0.8338 time to fit residues: 150.8879 Evaluate side-chains 118 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 81 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 142 MET Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 264 VAL Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 343 PHE Chi-restraints excluded: chain X residue 367 SER Chi-restraints excluded: chain X residue 387 LEU Chi-restraints excluded: chain X residue 397 ASP Chi-restraints excluded: chain X residue 430 VAL Chi-restraints excluded: chain X residue 473 LEU Chi-restraints excluded: chain X residue 477 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 199 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 171 GLN X 317 ASN H 13 GLN H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS L 201 GLN L 212 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.170465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128941 restraints weight = 28667.147| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 5.69 r_work: 0.3211 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7737 Z= 0.212 Angle : 0.649 9.700 10534 Z= 0.328 Chirality : 0.044 0.157 1162 Planarity : 0.006 0.083 1275 Dihedral : 11.849 59.880 1382 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.09 % Allowed : 12.80 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.26 (0.27), residues: 917 helix: -0.30 (0.28), residues: 343 sheet: -0.83 (0.36), residues: 201 loop : -3.05 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 93 HIS 0.004 0.001 HIS H 35 PHE 0.025 0.001 PHE X 343 TYR 0.011 0.001 TYR X 239 ARG 0.006 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 1.056 Fit side-chains REVERT: X 98 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8030 (tt) REVERT: X 167 ARG cc_start: 0.7715 (tmm160) cc_final: 0.6868 (ttp-110) REVERT: X 473 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8034 (mt) REVERT: X 530 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8588 (m-80) REVERT: H 46 GLU cc_start: 0.8712 (tt0) cc_final: 0.8480 (tt0) REVERT: H 205 CYS cc_start: 0.2937 (OUTLIER) cc_final: 0.2573 (t) REVERT: L 59 PRO cc_start: 0.8201 (Cg_exo) cc_final: 0.7866 (Cg_endo) outliers start: 41 outliers final: 19 residues processed: 123 average time/residue: 0.9942 time to fit residues: 131.3423 Evaluate side-chains 104 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 264 VAL Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 393 TYR Chi-restraints excluded: chain X residue 473 LEU Chi-restraints excluded: chain X residue 477 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 75 HIS X 291 HIS H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.168579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125778 restraints weight = 16620.224| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.44 r_work: 0.3277 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7737 Z= 0.264 Angle : 0.640 9.764 10534 Z= 0.322 Chirality : 0.044 0.149 1162 Planarity : 0.006 0.077 1275 Dihedral : 10.682 59.751 1352 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.98 % Allowed : 15.40 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.71 (0.28), residues: 917 helix: 0.09 (0.28), residues: 351 sheet: -0.43 (0.37), residues: 201 loop : -2.81 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 90 HIS 0.006 0.001 HIS H 35 PHE 0.025 0.001 PHE X 343 TYR 0.012 0.001 TYR X 281 ARG 0.007 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.857 Fit side-chains REVERT: X 98 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8040 (tt) REVERT: X 129 ARG cc_start: 0.8490 (ttm170) cc_final: 0.8204 (ttm170) REVERT: X 167 ARG cc_start: 0.7798 (tmm160) cc_final: 0.7006 (ttp-110) REVERT: X 387 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8099 (tp) REVERT: H 205 CYS cc_start: 0.2993 (OUTLIER) cc_final: 0.2588 (t) REVERT: L 59 PRO cc_start: 0.8194 (Cg_exo) cc_final: 0.7891 (Cg_endo) outliers start: 32 outliers final: 18 residues processed: 114 average time/residue: 1.0194 time to fit residues: 124.5895 Evaluate side-chains 106 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 264 VAL Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 387 LEU Chi-restraints excluded: chain X residue 393 TYR Chi-restraints excluded: chain X residue 477 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.0170 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 73 optimal weight: 0.0980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.173693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131127 restraints weight = 28551.145| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 5.66 r_work: 0.3238 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 7737 Z= 0.160 Angle : 0.565 8.404 10534 Z= 0.286 Chirality : 0.041 0.151 1162 Planarity : 0.005 0.076 1275 Dihedral : 9.610 57.588 1347 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.35 % Allowed : 16.40 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.03 (0.28), residues: 917 helix: 0.68 (0.29), residues: 344 sheet: -0.02 (0.38), residues: 200 loop : -2.42 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 90 HIS 0.004 0.001 HIS X 425 PHE 0.022 0.001 PHE X 343 TYR 0.008 0.001 TYR X 239 ARG 0.006 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.834 Fit side-chains REVERT: X 98 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.7906 (tt) REVERT: X 117 PHE cc_start: 0.8117 (t80) cc_final: 0.7847 (t80) REVERT: X 132 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7088 (mm-30) REVERT: X 167 ARG cc_start: 0.7849 (tmm160) cc_final: 0.7012 (ttp-110) REVERT: H 129 SER cc_start: 0.5966 (m) cc_final: 0.5612 (t) REVERT: H 205 CYS cc_start: 0.2978 (OUTLIER) cc_final: 0.2646 (t) outliers start: 27 outliers final: 19 residues processed: 104 average time/residue: 0.9933 time to fit residues: 111.3095 Evaluate side-chains 98 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain X residue 393 TYR Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 44 optimal weight: 0.0040 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.168802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.128733 restraints weight = 23221.312| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 4.98 r_work: 0.3184 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7737 Z= 0.197 Angle : 0.572 8.164 10534 Z= 0.289 Chirality : 0.042 0.144 1162 Planarity : 0.005 0.079 1275 Dihedral : 9.405 58.469 1344 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.35 % Allowed : 17.76 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.82 (0.28), residues: 917 helix: 0.76 (0.29), residues: 345 sheet: 0.14 (0.38), residues: 200 loop : -2.25 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 90 HIS 0.005 0.001 HIS H 35 PHE 0.023 0.001 PHE X 343 TYR 0.017 0.001 TYR H 154 ARG 0.006 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.712 Fit side-chains REVERT: X 98 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.7940 (tt) REVERT: X 117 PHE cc_start: 0.8027 (t80) cc_final: 0.7788 (t80) REVERT: X 132 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7050 (mm-30) REVERT: X 167 ARG cc_start: 0.7816 (tmm160) cc_final: 0.6938 (ttp-110) REVERT: H 129 SER cc_start: 0.5976 (m) cc_final: 0.5634 (t) REVERT: L 24 ARG cc_start: 0.7908 (ttp80) cc_final: 0.7410 (ttm110) REVERT: L 29 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8505 (t) outliers start: 27 outliers final: 19 residues processed: 107 average time/residue: 1.0363 time to fit residues: 118.9019 Evaluate side-chains 102 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 211 ILE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 307 ASP Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 393 TYR Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 70 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 186 GLN X 289 ASN H 76 ASN L 79 GLN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.167563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128207 restraints weight = 28965.897| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 5.60 r_work: 0.3123 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7737 Z= 0.250 Angle : 0.594 8.019 10534 Z= 0.302 Chirality : 0.043 0.141 1162 Planarity : 0.005 0.080 1275 Dihedral : 9.303 59.446 1341 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.48 % Allowed : 18.01 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.82 (0.28), residues: 917 helix: 0.67 (0.28), residues: 351 sheet: 0.17 (0.38), residues: 200 loop : -2.21 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 90 HIS 0.005 0.001 HIS H 35 PHE 0.025 0.001 PHE X 343 TYR 0.011 0.001 TYR X 428 ARG 0.005 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.756 Fit side-chains REVERT: X 98 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8056 (tt) REVERT: X 117 PHE cc_start: 0.8080 (t80) cc_final: 0.7847 (t80) REVERT: X 132 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7109 (mm-30) REVERT: X 167 ARG cc_start: 0.7876 (tmm160) cc_final: 0.6843 (ttp-110) REVERT: X 178 ILE cc_start: 0.7846 (mt) cc_final: 0.7626 (mm) REVERT: X 421 LYS cc_start: 0.8732 (ptmt) cc_final: 0.8143 (pttp) REVERT: H 88 GLU cc_start: 0.6918 (pp20) cc_final: 0.6715 (pp20) REVERT: H 129 SER cc_start: 0.6051 (m) cc_final: 0.5687 (t) REVERT: L 24 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7482 (ttm110) REVERT: L 29 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8545 (t) outliers start: 28 outliers final: 21 residues processed: 112 average time/residue: 0.9636 time to fit residues: 116.0622 Evaluate side-chains 110 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 307 ASP Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 378 HIS H 76 ASN L 79 GLN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.161191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120890 restraints weight = 25354.405| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 5.13 r_work: 0.3042 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 : 0.009 0.081 7737 Z= 0.594 Angle : 0.784 8.912 10534 Z= 0.399 Chirality : 0.052 0.163 1162 Planarity : 0.006 0.083 1275 Dihedral : 10.367 57.092 1341 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 5.09 % Allowed : 16.77 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.32 (0.28), residues: 917 helix: 0.13 (0.27), residues: 351 sheet: -0.16 (0.37), residues: 204 loop : -2.31 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 90 HIS 0.012 0.002 HIS H 35 PHE 0.030 0.002 PHE X 343 TYR 0.021 0.003 TYR H 185 ARG 0.005 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 0.770 Fit side-chains REVERT: X 98 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8303 (tt) REVERT: X 132 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: X 149 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.7998 (m) REVERT: X 167 ARG cc_start: 0.7903 (tmm160) cc_final: 0.6902 (ttp-110) REVERT: X 530 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.8572 (m-80) REVERT: L 24 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7624 (ttm110) REVERT: L 29 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8586 (t) outliers start: 41 outliers final: 21 residues processed: 112 average time/residue: 1.0123 time to fit residues: 121.6925 Evaluate side-chains 101 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 149 SER Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 369 SER Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain X residue 477 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 119 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.170860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128679 restraints weight = 22876.076| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 4.65 r_work: 0.3265 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7737 Z= 0.195 Angle : 0.592 8.440 10534 Z= 0.302 Chirality : 0.042 0.141 1162 Planarity : 0.006 0.080 1275 Dihedral : 9.548 58.768 1341 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.60 % Allowed : 18.88 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.78 (0.28), residues: 917 helix: 0.70 (0.28), residues: 351 sheet: 0.06 (0.38), residues: 201 loop : -2.10 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 90 HIS 0.006 0.001 HIS X 425 PHE 0.022 0.001 PHE X 343 TYR 0.011 0.001 TYR H 185 ARG 0.007 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.781 Fit side-chains REVERT: X 132 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7108 (mm-30) REVERT: X 167 ARG cc_start: 0.7888 (tmm160) cc_final: 0.6970 (ttp-110) REVERT: X 302 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8533 (ptm-80) REVERT: L 24 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7563 (ttm110) REVERT: L 29 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8521 (t) outliers start: 29 outliers final: 19 residues processed: 112 average time/residue: 0.9654 time to fit residues: 116.3813 Evaluate side-chains 106 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 211 ILE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 302 ARG Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain X residue 477 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 0.0000 chunk 80 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 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 = 0.3987 r_free = 0.3987 target = 0.170545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127358 restraints weight = 24935.589| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 4.97 r_work: 0.3220 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 7737 Z= 0.228 Angle : 0.938 59.199 10534 Z= 0.551 Chirality : 0.044 0.447 1162 Planarity : 0.006 0.082 1275 Dihedral : 9.392 58.771 1337 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.11 % Allowed : 19.01 % Favored : 77.89 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.28), residues: 917 helix: 0.74 (0.28), residues: 351 sheet: 0.08 (0.38), residues: 200 loop : -2.09 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 90 HIS 0.005 0.001 HIS X 425 PHE 0.023 0.001 PHE X 343 TYR 0.010 0.001 TYR H 185 ARG 0.006 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.680 Fit side-chains REVERT: X 132 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: X 167 ARG cc_start: 0.7903 (tmm160) cc_final: 0.6940 (ttp-110) REVERT: X 302 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8584 (ptm-80) REVERT: L 24 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7563 (ttm110) REVERT: L 29 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8549 (t) outliers start: 25 outliers final: 19 residues processed: 103 average time/residue: 1.0380 time to fit residues: 114.5051 Evaluate side-chains 106 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 211 ILE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 302 ARG Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain X residue 477 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 9 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 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 = 0.3987 r_free = 0.3987 target = 0.170571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130151 restraints weight = 29280.191| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 5.53 r_work: 0.3196 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 7737 Z= 0.228 Angle : 0.939 59.199 10534 Z= 0.551 Chirality : 0.044 0.447 1162 Planarity : 0.006 0.085 1275 Dihedral : 9.392 58.771 1337 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.73 % Allowed : 19.38 % Favored : 77.89 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.28), residues: 917 helix: 0.74 (0.28), residues: 351 sheet: 0.08 (0.38), residues: 200 loop : -2.09 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 90 HIS 0.005 0.001 HIS X 425 PHE 0.023 0.001 PHE X 343 TYR 0.010 0.001 TYR H 185 ARG 0.006 0.000 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.791 Fit side-chains REVERT: X 132 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7121 (mm-30) REVERT: X 167 ARG cc_start: 0.7889 (tmm160) cc_final: 0.6870 (ttp-110) REVERT: X 302 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8589 (ptm-80) REVERT: L 24 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7492 (ttm110) REVERT: L 29 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8549 (t) outliers start: 22 outliers final: 19 residues processed: 102 average time/residue: 1.0769 time to fit residues: 117.8309 Evaluate side-chains 106 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 211 ILE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 302 ARG Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain X residue 477 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 0.0270 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 24 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 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 = 0.3987 r_free = 0.3987 target = 0.170558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129226 restraints weight = 22007.158| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 4.70 r_work: 0.3263 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 7737 Z= 0.228 Angle : 0.939 59.199 10534 Z= 0.551 Chirality : 0.044 0.447 1162 Planarity : 0.006 0.085 1275 Dihedral : 9.392 58.771 1337 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.73 % Allowed : 19.38 % Favored : 77.89 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.28), residues: 917 helix: 0.74 (0.28), residues: 351 sheet: 0.08 (0.38), residues: 200 loop : -2.09 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 90 HIS 0.005 0.001 HIS X 425 PHE 0.023 0.001 PHE X 343 TYR 0.010 0.001 TYR H 185 ARG 0.006 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5693.85 seconds wall clock time: 101 minutes 17.13 seconds (6077.13 seconds total)