Starting phenix.real_space_refine on Wed Feb 4 03:07:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9drj_47127/02_2026/9drj_47127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9drj_47127/02_2026/9drj_47127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9drj_47127/02_2026/9drj_47127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9drj_47127/02_2026/9drj_47127.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9drj_47127/02_2026/9drj_47127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9drj_47127/02_2026/9drj_47127.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1 5.49 5 S 44 5.16 5 C 5415 2.51 5 N 1475 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8540 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2445 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 300} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4167 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 26, 'TRANS': 504} Chain breaks: 1 Chain: "C" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1277 Classifications: {'peptide': 159} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 142} Chain: "D" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 627 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3632 SG CYS B 158 41.504 34.986 61.172 1.00 3.63 S ATOM 3659 SG CYS B 161 45.325 34.774 61.351 1.00 24.35 S ATOM 5774 SG CYS B 441 43.135 34.725 64.479 1.00 31.81 S ATOM 5799 SG CYS B 444 43.292 31.706 62.159 1.00 19.04 S Time building chain proxies: 2.02, per 1000 atoms: 0.24 Number of scatterers: 8540 At special positions: 0 Unit cell: (84.133, 100.793, 114.954, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 44 16.00 P 1 15.00 O 1604 8.00 N 1475 7.00 C 5415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 173 " - pdb=" SG CYS C 93 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 319.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 441 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 158 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 161 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 444 " Number of angles added : 6 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 5 sheets defined 46.7% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 12 through 27 removed outlier: 5.710A pdb=" N ARG A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 36 Processing helix chain 'A' and resid 45 through 59 Processing helix chain 'A' and resid 90 through 103 removed outlier: 4.499A pdb=" N GLU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARG A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 4.069A pdb=" N PHE A 123 " --> pdb=" O PRO A 119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 124' Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 238 through 254 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 261 through 280 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 288 through 294 removed outlier: 4.177A pdb=" N VAL A 292 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 320 Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 53 through 59 removed outlier: 3.681A pdb=" N LEU B 57 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN B 58 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.595A pdb=" N VAL B 68 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 84 removed outlier: 3.965A pdb=" N PHE B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 118 through 133 Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.799A pdb=" N ARG B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 198 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 239 through 248 Processing helix chain 'B' and resid 250 through 260 Processing helix chain 'B' and resid 260 through 269 removed outlier: 4.158A pdb=" N MET B 269 " --> pdb=" O TYR B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.632A pdb=" N TRP B 273 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 274 " --> pdb=" O LYS B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 274' Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.849A pdb=" N GLN B 311 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 336 Processing helix chain 'B' and resid 337 through 340 Processing helix chain 'B' and resid 348 through 366 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 387 through 407 removed outlier: 3.593A pdb=" N ASN B 391 " --> pdb=" O ILE B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 412 Processing helix chain 'B' and resid 456 through 459 removed outlier: 3.710A pdb=" N VAL B 459 " --> pdb=" O VAL B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 456 through 459' Processing helix chain 'B' and resid 460 through 467 Processing helix chain 'B' and resid 505 through 510 Processing helix chain 'C' and resid 2 through 19 Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 108 through 122 Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 140 through 155 removed outlier: 3.721A pdb=" N TYR C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 56 Processing helix chain 'D' and resid 76 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 6.330A pdb=" N LEU A 63 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP A 111 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N MET A 65 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 39 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU A 66 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 41 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG A 38 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N CYS A 130 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 40 " --> pdb=" O CYS A 130 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR A 132 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL A 42 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL A 129 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLY A 156 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU A 131 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N VAL A 158 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY A 338 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ARG B 414 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N THR B 150 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 146 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER B 139 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ARG B 19 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N MET B 113 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 21 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 177 Processing sheet with id=AA3, first strand: chain 'B' and resid 544 through 547 removed outlier: 4.518A pdb=" N THR B 451 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE B 482 " --> pdb=" O ILE B 489 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE B 489 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN C 40 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 544 through 547 removed outlier: 4.518A pdb=" N THR B 451 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE B 482 " --> pdb=" O ILE B 489 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE B 489 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 33 through 38 removed outlier: 3.625A pdb=" N ASP D 86 " --> pdb=" O LYS D 23 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2835 1.34 - 1.46: 1510 1.46 - 1.58: 4299 1.58 - 1.69: 1 1.69 - 1.81: 66 Bond restraints: 8711 Sorted by residual: bond pdb=" CA GLU B 218 " pdb=" CB GLU B 218 " ideal model delta sigma weight residual 1.525 1.538 -0.013 8.30e-03 1.45e+04 2.47e+00 bond pdb=" C4' AMP D 601 " pdb=" O4' AMP D 601 " ideal model delta sigma weight residual 1.426 1.456 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C2' AMP D 601 " pdb=" O2' AMP D 601 " ideal model delta sigma weight residual 1.432 1.410 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" CB PRO A 284 " pdb=" CG PRO A 284 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.10e+00 bond pdb=" CA PRO C 123 " pdb=" C PRO C 123 " ideal model delta sigma weight residual 1.525 1.517 0.009 9.70e-03 1.06e+04 8.11e-01 ... (remaining 8706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 11626 1.96 - 3.92: 126 3.92 - 5.89: 17 5.89 - 7.85: 4 7.85 - 9.81: 2 Bond angle restraints: 11775 Sorted by residual: angle pdb=" C1' AMP D 601 " pdb=" C2' AMP D 601 " pdb=" C3' AMP D 601 " ideal model delta sigma weight residual 111.00 101.19 9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CA GLU C 122 " pdb=" CB GLU C 122 " pdb=" CG GLU C 122 " ideal model delta sigma weight residual 114.10 119.90 -5.80 2.00e+00 2.50e-01 8.40e+00 angle pdb=" C GLU C 122 " pdb=" CA GLU C 122 " pdb=" CB GLU C 122 " ideal model delta sigma weight residual 110.16 113.84 -3.68 1.33e+00 5.65e-01 7.67e+00 angle pdb=" C2' AMP D 601 " pdb=" C3' AMP D 601 " pdb=" C4' AMP D 601 " ideal model delta sigma weight residual 111.00 103.09 7.91 3.00e+00 1.11e-01 6.96e+00 angle pdb=" C TRP B 217 " pdb=" N GLU B 218 " pdb=" CA GLU B 218 " ideal model delta sigma weight residual 124.21 127.09 -2.88 1.21e+00 6.83e-01 5.66e+00 ... (remaining 11770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.64: 4768 23.64 - 47.28: 446 47.28 - 70.91: 89 70.91 - 94.55: 14 94.55 - 118.19: 1 Dihedral angle restraints: 5318 sinusoidal: 2199 harmonic: 3119 Sorted by residual: dihedral pdb=" C2' AMP D 601 " pdb=" C1' AMP D 601 " pdb=" N9 AMP D 601 " pdb=" C4 AMP D 601 " ideal model delta sinusoidal sigma weight residual 91.55 -26.64 118.19 1 2.00e+01 2.50e-03 3.53e+01 dihedral pdb=" C4' AMP D 601 " pdb=" C5' AMP D 601 " pdb=" O5' AMP D 601 " pdb=" P AMP D 601 " ideal model delta sinusoidal sigma weight residual -180.00 -94.30 -85.70 1 2.00e+01 2.50e-03 2.22e+01 dihedral pdb=" CA ASP B 212 " pdb=" C ASP B 212 " pdb=" N PRO B 213 " pdb=" CA PRO B 213 " ideal model delta harmonic sigma weight residual -180.00 -160.58 -19.42 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 5315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1056 0.048 - 0.096: 193 0.096 - 0.145: 56 0.145 - 0.193: 0 0.193 - 0.241: 1 Chirality restraints: 1306 Sorted by residual: chirality pdb=" C3' AMP D 601 " pdb=" C2' AMP D 601 " pdb=" C4' AMP D 601 " pdb=" O3' AMP D 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE D 88 " pdb=" N ILE D 88 " pdb=" C ILE D 88 " pdb=" CB ILE D 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA TRP A 26 " pdb=" N TRP A 26 " pdb=" C TRP A 26 " pdb=" CB TRP A 26 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1303 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 283 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO A 284 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 344 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 345 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 87 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO C 88 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 88 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 88 " 0.025 5.00e-02 4.00e+02 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 303 2.72 - 3.27: 8301 3.27 - 3.81: 14383 3.81 - 4.36: 17910 4.36 - 4.90: 30611 Nonbonded interactions: 71508 Sorted by model distance: nonbonded pdb=" OH TYR B 265 " pdb=" O GLN C 130 " model vdw 2.175 3.040 nonbonded pdb=" OE2 GLU C 12 " pdb=" OG1 THR C 108 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 317 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR B 169 " pdb=" OE2 GLU C 99 " model vdw 2.250 3.040 nonbonded pdb=" O PHE A 296 " pdb=" OG SER A 297 " model vdw 2.257 3.040 ... (remaining 71503 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=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: 1.120 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.210 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 0.003 0.133 8717 Z= 0.180 Angle : 0.516 9.810 11783 Z= 0.251 Chirality : 0.040 0.241 1306 Planarity : 0.004 0.077 1531 Dihedral : 18.288 118.191 3295 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.32 % Allowed : 28.25 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.26), residues: 1068 helix: 1.59 (0.25), residues: 442 sheet: 0.41 (0.37), residues: 201 loop : 0.60 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 274 TYR 0.011 0.001 TYR B 265 PHE 0.011 0.001 PHE C 82 TRP 0.009 0.001 TRP A 26 HIS 0.001 0.000 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8711) covalent geometry : angle 0.51323 (11775) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.24003 ( 2) hydrogen bonds : bond 0.16815 ( 411) hydrogen bonds : angle 6.54836 ( 1206) metal coordination : bond 0.00422 ( 4) metal coordination : angle 2.22671 ( 6) Misc. bond : bond 0.13252 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: D 86 ASP cc_start: 0.8840 (t70) cc_final: 0.8382 (t70) outliers start: 3 outliers final: 2 residues processed: 123 average time/residue: 0.5590 time to fit residues: 73.0782 Evaluate side-chains 103 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain C residue 66 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS B 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.083713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.059302 restraints weight = 16010.354| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.36 r_work: 0.2606 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8717 Z= 0.135 Angle : 0.593 9.599 11783 Z= 0.292 Chirality : 0.042 0.146 1306 Planarity : 0.004 0.051 1531 Dihedral : 6.208 122.736 1165 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.54 % Allowed : 26.53 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.27), residues: 1068 helix: 1.81 (0.25), residues: 440 sheet: 0.38 (0.37), residues: 200 loop : 0.78 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 293 TYR 0.022 0.001 TYR B 265 PHE 0.010 0.001 PHE B 83 TRP 0.007 0.001 TRP A 26 HIS 0.002 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8711) covalent geometry : angle 0.58997 (11775) SS BOND : bond 0.00222 ( 1) SS BOND : angle 0.39461 ( 2) hydrogen bonds : bond 0.04075 ( 411) hydrogen bonds : angle 5.10925 ( 1206) metal coordination : bond 0.00638 ( 4) metal coordination : angle 2.63724 ( 6) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.236 Fit side-chains REVERT: A 159 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7233 (p90) REVERT: B 97 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8043 (mmm) REVERT: C 122 GLU cc_start: 0.7747 (pp20) cc_final: 0.7526 (pp20) REVERT: D 45 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8356 (tptp) REVERT: D 60 ASN cc_start: 0.8709 (t0) cc_final: 0.8290 (t0) REVERT: D 78 LYS cc_start: 0.9368 (mmpt) cc_final: 0.9081 (mmpt) outliers start: 33 outliers final: 10 residues processed: 130 average time/residue: 0.6014 time to fit residues: 82.8182 Evaluate side-chains 108 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 90 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.083679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.059255 restraints weight = 15853.938| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.35 r_work: 0.2631 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8717 Z= 0.123 Angle : 0.589 9.190 11783 Z= 0.288 Chirality : 0.042 0.197 1306 Planarity : 0.004 0.049 1531 Dihedral : 5.545 123.691 1165 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.93 % Allowed : 28.03 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.27), residues: 1068 helix: 1.94 (0.25), residues: 433 sheet: 0.24 (0.37), residues: 201 loop : 0.71 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 33 TYR 0.019 0.001 TYR A 262 PHE 0.012 0.001 PHE D 36 TRP 0.007 0.001 TRP A 26 HIS 0.003 0.000 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8711) covalent geometry : angle 0.58690 (11775) SS BOND : bond 0.00204 ( 1) SS BOND : angle 0.47274 ( 2) hydrogen bonds : bond 0.03676 ( 411) hydrogen bonds : angle 4.79229 ( 1206) metal coordination : bond 0.00555 ( 4) metal coordination : angle 2.51912 ( 6) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 159 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7296 (p90) REVERT: A 228 LYS cc_start: 0.9191 (ptmt) cc_final: 0.8990 (mppt) REVERT: A 235 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.8072 (mtm-85) REVERT: B 168 ARG cc_start: 0.8555 (tpt-90) cc_final: 0.8341 (tpp80) REVERT: C 122 GLU cc_start: 0.7838 (pp20) cc_final: 0.7454 (pp20) REVERT: D 45 LYS cc_start: 0.9140 (tmtt) cc_final: 0.8682 (tptp) REVERT: D 60 ASN cc_start: 0.8683 (t0) cc_final: 0.8140 (t0) REVERT: D 73 ASP cc_start: 0.9025 (m-30) cc_final: 0.8824 (t0) outliers start: 18 outliers final: 9 residues processed: 120 average time/residue: 0.6298 time to fit residues: 80.2522 Evaluate side-chains 108 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 90 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 52 optimal weight: 0.0020 chunk 12 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN C 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.082999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.058552 restraints weight = 16120.437| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.38 r_work: 0.2616 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8717 Z= 0.130 Angle : 0.587 8.762 11783 Z= 0.283 Chirality : 0.042 0.184 1306 Planarity : 0.004 0.049 1531 Dihedral : 5.478 123.654 1163 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.47 % Allowed : 28.57 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.27), residues: 1068 helix: 1.98 (0.25), residues: 433 sheet: 0.10 (0.36), residues: 201 loop : 0.73 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.020 0.001 TYR C 87 PHE 0.013 0.001 PHE D 36 TRP 0.007 0.001 TRP B 217 HIS 0.002 0.000 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8711) covalent geometry : angle 0.58406 (11775) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.53339 ( 2) hydrogen bonds : bond 0.03502 ( 411) hydrogen bonds : angle 4.66611 ( 1206) metal coordination : bond 0.00634 ( 4) metal coordination : angle 2.61756 ( 6) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8309 (mtm-85) cc_final: 0.8104 (mtm-85) REVERT: B 97 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8499 (mtm) REVERT: B 168 ARG cc_start: 0.8614 (tpt-90) cc_final: 0.8236 (tpt-90) REVERT: B 522 PHE cc_start: 0.6126 (m-80) cc_final: 0.5924 (m-10) REVERT: C 122 GLU cc_start: 0.7917 (pp20) cc_final: 0.7502 (pp20) REVERT: D 45 LYS cc_start: 0.9141 (tmtt) cc_final: 0.8672 (tptp) REVERT: D 59 MET cc_start: 0.7600 (pmm) cc_final: 0.6784 (ppp) REVERT: D 60 ASN cc_start: 0.8637 (t0) cc_final: 0.8303 (t0) outliers start: 23 outliers final: 11 residues processed: 118 average time/residue: 0.5736 time to fit residues: 72.1141 Evaluate side-chains 108 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain D residue 90 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 88 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.083298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.059065 restraints weight = 16039.290| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.36 r_work: 0.2630 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8717 Z= 0.117 Angle : 0.583 8.922 11783 Z= 0.280 Chirality : 0.041 0.168 1306 Planarity : 0.004 0.051 1531 Dihedral : 5.413 122.269 1163 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.04 % Allowed : 28.68 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.27), residues: 1068 helix: 1.99 (0.25), residues: 433 sheet: 0.12 (0.37), residues: 201 loop : 0.71 (0.33), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 70 TYR 0.019 0.001 TYR A 262 PHE 0.021 0.001 PHE D 66 TRP 0.007 0.001 TRP A 26 HIS 0.002 0.000 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8711) covalent geometry : angle 0.58062 (11775) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.49131 ( 2) hydrogen bonds : bond 0.03306 ( 411) hydrogen bonds : angle 4.55649 ( 1206) metal coordination : bond 0.00517 ( 4) metal coordination : angle 2.47526 ( 6) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8466 (mtm) REVERT: B 269 MET cc_start: 0.8018 (mtt) cc_final: 0.7452 (mtt) REVERT: B 522 PHE cc_start: 0.6177 (m-80) cc_final: 0.5905 (m-10) REVERT: C 62 MET cc_start: 0.8915 (mtt) cc_final: 0.8688 (mtt) REVERT: C 122 GLU cc_start: 0.7910 (pp20) cc_final: 0.7507 (pp20) REVERT: D 45 LYS cc_start: 0.9101 (tmtt) cc_final: 0.8624 (tptp) REVERT: D 59 MET cc_start: 0.7499 (pmm) cc_final: 0.6632 (ppp) REVERT: D 60 ASN cc_start: 0.8561 (t0) cc_final: 0.8232 (t0) outliers start: 19 outliers final: 10 residues processed: 115 average time/residue: 0.5181 time to fit residues: 63.4986 Evaluate side-chains 109 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain D residue 90 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 81 optimal weight: 0.0020 chunk 90 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 0.0770 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.5346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 531 ASN D 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.083839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.059703 restraints weight = 15987.691| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.37 r_work: 0.2624 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8717 Z= 0.111 Angle : 0.575 8.982 11783 Z= 0.277 Chirality : 0.041 0.160 1306 Planarity : 0.004 0.050 1531 Dihedral : 5.380 120.930 1163 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.36 % Allowed : 28.89 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.27), residues: 1068 helix: 1.85 (0.25), residues: 441 sheet: 0.17 (0.37), residues: 201 loop : 0.64 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 168 TYR 0.020 0.001 TYR C 87 PHE 0.031 0.001 PHE D 66 TRP 0.008 0.001 TRP A 26 HIS 0.002 0.000 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8711) covalent geometry : angle 0.57256 (11775) SS BOND : bond 0.00311 ( 1) SS BOND : angle 0.64453 ( 2) hydrogen bonds : bond 0.03188 ( 411) hydrogen bonds : angle 4.50538 ( 1206) metal coordination : bond 0.00435 ( 4) metal coordination : angle 2.34753 ( 6) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8459 (mtm) REVERT: B 168 ARG cc_start: 0.8582 (tpt-90) cc_final: 0.8153 (tpt-90) REVERT: B 269 MET cc_start: 0.8029 (mtt) cc_final: 0.7573 (mtt) REVERT: B 522 PHE cc_start: 0.6183 (m-80) cc_final: 0.5916 (m-10) REVERT: C 122 GLU cc_start: 0.7926 (pp20) cc_final: 0.7509 (pp20) REVERT: D 46 LYS cc_start: 0.8307 (mmtm) cc_final: 0.8002 (mptt) REVERT: D 59 MET cc_start: 0.7561 (pmm) cc_final: 0.6718 (ppp) REVERT: D 60 ASN cc_start: 0.8519 (t0) cc_final: 0.8170 (t0) outliers start: 22 outliers final: 10 residues processed: 118 average time/residue: 0.5272 time to fit residues: 66.6019 Evaluate side-chains 110 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 90 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 0.0000 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.083120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.059259 restraints weight = 16587.157| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.39 r_work: 0.2642 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8717 Z= 0.109 Angle : 0.580 9.694 11783 Z= 0.278 Chirality : 0.041 0.152 1306 Planarity : 0.004 0.051 1531 Dihedral : 5.299 119.658 1163 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.26 % Allowed : 29.54 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.27), residues: 1068 helix: 1.88 (0.25), residues: 440 sheet: 0.22 (0.38), residues: 201 loop : 0.64 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 235 TYR 0.018 0.001 TYR B 265 PHE 0.016 0.001 PHE D 66 TRP 0.007 0.001 TRP A 26 HIS 0.002 0.000 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8711) covalent geometry : angle 0.57789 (11775) SS BOND : bond 0.00538 ( 1) SS BOND : angle 0.31767 ( 2) hydrogen bonds : bond 0.03108 ( 411) hydrogen bonds : angle 4.45587 ( 1206) metal coordination : bond 0.00427 ( 4) metal coordination : angle 2.25697 ( 6) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8467 (mtm) REVERT: B 168 ARG cc_start: 0.8603 (tpt-90) cc_final: 0.8264 (tpp80) REVERT: B 269 MET cc_start: 0.8023 (mtt) cc_final: 0.7635 (mtt) REVERT: B 522 PHE cc_start: 0.6301 (m-80) cc_final: 0.6018 (m-10) REVERT: C 122 GLU cc_start: 0.7956 (pp20) cc_final: 0.7573 (pp20) REVERT: D 23 LYS cc_start: 0.7941 (tppp) cc_final: 0.7721 (tppp) REVERT: D 39 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8324 (mmmt) REVERT: D 40 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7701 (mpt) REVERT: D 59 MET cc_start: 0.7634 (pmm) cc_final: 0.6819 (ppp) REVERT: D 60 ASN cc_start: 0.8452 (t0) cc_final: 0.8145 (t0) outliers start: 21 outliers final: 11 residues processed: 119 average time/residue: 0.4755 time to fit residues: 60.6209 Evaluate side-chains 113 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 90 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN B 58 ASN D 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.081551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.057447 restraints weight = 16165.716| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.35 r_work: 0.2595 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8717 Z= 0.196 Angle : 0.620 10.121 11783 Z= 0.298 Chirality : 0.043 0.143 1306 Planarity : 0.004 0.051 1531 Dihedral : 5.427 122.062 1163 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.93 % Allowed : 29.86 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.27), residues: 1068 helix: 1.91 (0.25), residues: 439 sheet: 0.08 (0.37), residues: 201 loop : 0.63 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 168 TYR 0.022 0.002 TYR C 87 PHE 0.017 0.001 PHE D 66 TRP 0.008 0.001 TRP B 344 HIS 0.002 0.000 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 8711) covalent geometry : angle 0.61709 (11775) SS BOND : bond 0.00397 ( 1) SS BOND : angle 0.74682 ( 2) hydrogen bonds : bond 0.03527 ( 411) hydrogen bonds : angle 4.58631 ( 1206) metal coordination : bond 0.00932 ( 4) metal coordination : angle 2.75339 ( 6) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8253 (mtm) REVERT: B 168 ARG cc_start: 0.8658 (tpt-90) cc_final: 0.8174 (tpt-90) REVERT: C 54 GLU cc_start: 0.8315 (pt0) cc_final: 0.7768 (pm20) REVERT: C 122 GLU cc_start: 0.8022 (pp20) cc_final: 0.7635 (pp20) REVERT: D 23 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7691 (tppp) REVERT: D 40 MET cc_start: 0.8245 (mmm) cc_final: 0.7632 (mpp) REVERT: D 59 MET cc_start: 0.7669 (pmm) cc_final: 0.6825 (ppp) outliers start: 18 outliers final: 11 residues processed: 112 average time/residue: 0.5622 time to fit residues: 67.2555 Evaluate side-chains 109 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 90 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN B 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.057469 restraints weight = 16540.841| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.34 r_work: 0.2576 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8717 Z= 0.150 Angle : 0.625 11.357 11783 Z= 0.298 Chirality : 0.042 0.161 1306 Planarity : 0.004 0.051 1531 Dihedral : 5.424 121.729 1163 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.50 % Allowed : 30.61 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.27), residues: 1068 helix: 1.87 (0.25), residues: 439 sheet: 0.05 (0.38), residues: 201 loop : 0.65 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 59 TYR 0.020 0.002 TYR C 87 PHE 0.022 0.001 PHE D 66 TRP 0.009 0.001 TRP B 217 HIS 0.002 0.000 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8711) covalent geometry : angle 0.62210 (11775) SS BOND : bond 0.00386 ( 1) SS BOND : angle 0.64595 ( 2) hydrogen bonds : bond 0.03416 ( 411) hydrogen bonds : angle 4.55766 ( 1206) metal coordination : bond 0.00777 ( 4) metal coordination : angle 2.73441 ( 6) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8264 (mtm) REVERT: B 168 ARG cc_start: 0.8653 (tpt-90) cc_final: 0.8150 (tpt-90) REVERT: C 54 GLU cc_start: 0.8324 (pt0) cc_final: 0.7777 (pm20) REVERT: C 122 GLU cc_start: 0.8048 (pp20) cc_final: 0.7672 (pp20) REVERT: D 23 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7718 (tppp) REVERT: D 40 MET cc_start: 0.8269 (mmm) cc_final: 0.7655 (mpt) REVERT: D 60 ASN cc_start: 0.8452 (t0) cc_final: 0.7796 (t0) outliers start: 14 outliers final: 12 residues processed: 111 average time/residue: 0.4974 time to fit residues: 59.0679 Evaluate side-chains 112 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.080941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.057250 restraints weight = 16563.606| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.35 r_work: 0.2597 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8717 Z= 0.155 Angle : 0.633 11.868 11783 Z= 0.301 Chirality : 0.043 0.189 1306 Planarity : 0.004 0.048 1531 Dihedral : 5.426 121.731 1163 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.61 % Allowed : 30.40 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.27), residues: 1068 helix: 1.85 (0.25), residues: 439 sheet: 0.00 (0.37), residues: 202 loop : 0.64 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 235 TYR 0.024 0.002 TYR C 87 PHE 0.028 0.001 PHE D 66 TRP 0.009 0.001 TRP B 217 HIS 0.002 0.000 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8711) covalent geometry : angle 0.62971 (11775) SS BOND : bond 0.00378 ( 1) SS BOND : angle 0.61945 ( 2) hydrogen bonds : bond 0.03422 ( 411) hydrogen bonds : angle 4.55348 ( 1206) metal coordination : bond 0.00779 ( 4) metal coordination : angle 2.72158 ( 6) Misc. bond : bond 0.00011 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8269 (mtm) REVERT: B 168 ARG cc_start: 0.8667 (tpt-90) cc_final: 0.8157 (tpt-90) REVERT: C 54 GLU cc_start: 0.8317 (pt0) cc_final: 0.7783 (pm20) REVERT: C 122 GLU cc_start: 0.8056 (pp20) cc_final: 0.7685 (pp20) REVERT: D 23 LYS cc_start: 0.7951 (tppp) cc_final: 0.7735 (tppp) REVERT: D 59 MET cc_start: 0.7644 (pmm) cc_final: 0.6924 (ppp) REVERT: D 60 ASN cc_start: 0.8468 (t0) cc_final: 0.8162 (t0) outliers start: 15 outliers final: 13 residues processed: 112 average time/residue: 0.5757 time to fit residues: 68.7387 Evaluate side-chains 112 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain D residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 0.0570 chunk 39 optimal weight: 3.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.081145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.057442 restraints weight = 16535.421| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.35 r_work: 0.2570 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8717 Z= 0.142 Angle : 0.625 11.824 11783 Z= 0.298 Chirality : 0.042 0.161 1306 Planarity : 0.004 0.048 1531 Dihedral : 5.417 121.424 1163 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.72 % Allowed : 30.08 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.27), residues: 1068 helix: 1.85 (0.25), residues: 439 sheet: 0.02 (0.38), residues: 202 loop : 0.65 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 168 TYR 0.023 0.002 TYR C 87 PHE 0.027 0.001 PHE D 66 TRP 0.008 0.001 TRP B 217 HIS 0.006 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8711) covalent geometry : angle 0.62241 (11775) SS BOND : bond 0.00371 ( 1) SS BOND : angle 0.59532 ( 2) hydrogen bonds : bond 0.03375 ( 411) hydrogen bonds : angle 4.51921 ( 1206) metal coordination : bond 0.00706 ( 4) metal coordination : angle 2.65410 ( 6) Misc. bond : bond 0.00013 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2468.58 seconds wall clock time: 42 minutes 55.23 seconds (2575.23 seconds total)