Starting phenix.real_space_refine on Wed Aug 5 05:09:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9drj_47127/08_2026/9drj_47127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9drj_47127/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9drj_47127/08_2026/9drj_47127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9drj_47127/08_2026/9drj_47127.map" model { file = "/net/cci-nas-00/data/ceres_data/9drj_47127/08_2026/9drj_47127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9drj_47127/08_2026/9drj_47127.cif" } 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-2.2rc3-6140/lib/python3.11/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: 2.01, 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: 0.70 Conformation dependent library (CDL) restraints added in 469.0 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: 0.27 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: 1.55 Time building geometry restraints manager: 0.93 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=" 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 bond pdb=" C4 AMP D 601 " pdb=" C5 AMP D 601 " ideal model delta sigma weight residual 1.490 1.474 0.016 2.00e-02 2.50e+03 6.50e-01 bond pdb=" CB GLU C 122 " pdb=" CG GLU C 122 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.81e-01 ... (remaining 8706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 11568 1.53 - 3.06: 168 3.06 - 4.59: 29 4.59 - 6.12: 7 6.12 - 7.64: 3 Bond angle restraints: 11775 Sorted by residual: 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=" 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 angle pdb=" CA LEU B 272 " pdb=" CB LEU B 272 " pdb=" CG LEU B 272 " ideal model delta sigma weight residual 116.30 123.94 -7.64 3.50e+00 8.16e-02 4.77e+00 angle pdb=" O1P AMP D 601 " pdb=" P AMP D 601 " pdb=" O2P AMP D 601 " ideal model delta sigma weight residual 119.90 113.42 6.48 3.00e+00 1.11e-01 4.66e+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: 13 94.55 - 118.19: 2 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=" 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 dihedral pdb=" CA ASP A 20 " pdb=" CB ASP A 20 " pdb=" CG ASP A 20 " pdb=" OD1 ASP A 20 " ideal model delta sinusoidal sigma weight residual -30.00 -89.69 59.69 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 5315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 743 0.026 - 0.051: 349 0.051 - 0.077: 120 0.077 - 0.103: 58 0.103 - 0.129: 36 Chirality restraints: 1306 Sorted by residual: 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 chirality pdb=" CA VAL B 148 " pdb=" N VAL B 148 " pdb=" C VAL B 148 " pdb=" CB VAL B 148 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.94e-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: 1.330 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: 0.030 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.270 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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= 0.179 Angle : 0.493 7.645 11783 Z= 0.246 Chirality : 0.040 0.129 1306 Planarity : 0.004 0.077 1531 Dihedral : 18.302 118.191 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/Z covalent geometry : bond 0.00245 / 0.11 ( 8711) covalent geometry : angle 0.49017 / 0.25 (11775) SS BOND : bond 0.00006 / 0.00 ( 1) SS BOND : angle 0.24003 / 0.08 ( 2) hydrogen bonds : bond 0.16815 / 11.61 ( 411) hydrogen bonds : angle 6.54836 / 4.64 ( 1206) metal coordination : bond 0.00422 / 0.22 ( 4) metal coordination : angle 2.22671 / 0.89 ( 6) Misc. bond : bond 0.13252 / 8.28 ( 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 : 0.250 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: 0.5223 time to fit residues: 68.3389 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 : 0.314 ------------------------------------------------------------------------------- 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... A 162 HIS A 312 GLN B 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.083760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.059315 restraints weight = 16007.865| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.35 r_work: 0.2630 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8717 Z= 0.133 Angle : 0.580 9.638 11783 Z= 0.288 Chirality : 0.042 0.138 1306 Planarity : 0.004 0.051 1531 Dihedral : 6.637 116.680 1165 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.65 % Allowed : 26.42 % 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 D 70 TYR 0.021 0.001 TYR B 265 PHE 0.011 0.001 PHE B 83 TRP 0.007 0.001 TRP B 344 HIS 0.002 0.000 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8711) covalent geometry : angle 0.57752 / 0.29 (11775) SS BOND : bond 0.00224 / 0.14 ( 1) SS BOND : angle 0.43540 / 0.20 ( 2) hydrogen bonds : bond 0.04113 / 2.79 ( 411) hydrogen bonds : angle 5.09984 / 3.61 ( 1206) metal coordination : bond 0.00655 / 0.35 ( 4) metal coordination : angle 2.64793 / 1.04 ( 6) Misc. bond : bond 0.00019 / 0.01 ( 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 139 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.318 Fit side-chains REVERT: A 159 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7252 (p90) REVERT: B 97 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8045 (mmm) REVERT: C 122 GLU cc_start: 0.7744 (pp20) cc_final: 0.7524 (pp20) REVERT: D 36 PHE cc_start: 0.8135 (m-80) cc_final: 0.7915 (m-80) REVERT: D 45 LYS cc_start: 0.9020 (tmtt) cc_final: 0.8373 (tptp) REVERT: D 60 ASN cc_start: 0.8733 (t0) cc_final: 0.8316 (t0) REVERT: D 78 LYS cc_start: 0.9373 (mmpt) cc_final: 0.9097 (mmpt) outliers start: 34 outliers final: 10 residues processed: 131 average time/residue: 0.5414 time to fit residues: 75.6541 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 : 0.255 ------------------------------------------------------------------------------- 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: 0.0000 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.083841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.059364 restraints weight = 15839.473| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.35 r_work: 0.2633 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1474 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= 0.120 Angle : 0.576 9.382 11783 Z= 0.284 Chirality : 0.041 0.200 1306 Planarity : 0.004 0.049 1531 Dihedral : 6.087 115.313 1165 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.72 % Allowed : 28.14 % Favored : 70.14 % 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: 1.93 (0.25), residues: 433 sheet: 0.25 (0.37), residues: 201 loop : 0.72 (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 0.009 0.001 PHE C 82 TRP 0.007 0.001 TRP A 26 HIS 0.003 0.000 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8711) covalent geometry : angle 0.57308 / 0.28 (11775) SS BOND : bond 0.00207 / 0.13 ( 1) SS BOND : angle 0.46904 / 0.22 ( 2) hydrogen bonds : bond 0.03647 / 2.49 ( 411) hydrogen bonds : angle 4.78837 / 3.38 ( 1206) metal coordination : bond 0.00534 / 0.29 ( 4) metal coordination : angle 2.48537 / 0.94 ( 6) Misc. bond : bond 0.00010 / 0.01 ( 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 123 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 299 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7912 (mtm) REVERT: C 122 GLU cc_start: 0.7834 (pp20) cc_final: 0.7452 (pp20) REVERT: D 45 LYS cc_start: 0.9127 (tmtt) cc_final: 0.8639 (tptp) REVERT: D 60 ASN cc_start: 0.8679 (t0) cc_final: 0.8135 (t0) outliers start: 16 outliers final: 8 residues processed: 118 average time/residue: 0.5426 time to fit residues: 67.9203 Evaluate side-chains 107 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 299 MET 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 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: 0.0040 chunk 10 optimal weight: 0.0030 chunk 52 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3160 r_free = 0.3160 target = 0.081827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.057352 restraints weight = 16218.937| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.36 r_work: 0.2590 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8717 Z= 0.171 Angle : 0.602 8.912 11783 Z= 0.294 Chirality : 0.043 0.185 1306 Planarity : 0.004 0.049 1531 Dihedral : 6.112 116.538 1163 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.69 % Allowed : 28.89 % Favored : 68.42 % 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: 1.54 (0.27), residues: 1068 helix: 1.94 (0.25), residues: 433 sheet: 0.06 (0.36), residues: 201 loop : 0.73 (0.33), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 168 TYR 0.021 0.001 TYR C 87 PHE 0.013 0.001 PHE B 83 TRP 0.007 0.001 TRP B 344 HIS 0.002 0.001 HIS B 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 8711) covalent geometry : angle 0.59798 / 0.29 (11775) SS BOND : bond 0.00234 / 0.15 ( 1) SS BOND : angle 0.58004 / 0.27 ( 2) hydrogen bonds : bond 0.03767 / 2.57 ( 411) hydrogen bonds : angle 4.74096 / 3.36 ( 1206) metal coordination : bond 0.00854 / 0.46 ( 4) metal coordination : angle 2.94560 / 1.11 ( 6) Misc. bond : bond 0.00019 / 0.01 ( 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 124 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.8057 (mtm-85) REVERT: B 97 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8525 (mtm) REVERT: B 522 PHE cc_start: 0.6208 (m-80) cc_final: 0.5909 (m-10) REVERT: C 122 GLU cc_start: 0.7964 (pp20) cc_final: 0.7556 (pp20) REVERT: D 45 LYS cc_start: 0.9090 (tmtt) cc_final: 0.8624 (tptp) REVERT: D 59 MET cc_start: 0.7560 (pmm) cc_final: 0.6718 (ppp) REVERT: D 60 ASN cc_start: 0.8651 (t0) cc_final: 0.8341 (t0) outliers start: 25 outliers final: 13 residues processed: 119 average time/residue: 0.5145 time to fit residues: 65.0634 Evaluate side-chains 109 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL 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 50 SER 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: 0.9990 chunk 81 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 91 optimal weight: 0.0370 chunk 42 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3173 r_free = 0.3173 target = 0.082589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.058336 restraints weight = 16073.832| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.36 r_work: 0.2621 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 0.034 8717 Z= 0.122 Angle : 0.577 8.859 11783 Z= 0.280 Chirality : 0.041 0.171 1306 Planarity : 0.004 0.050 1531 Dihedral : 6.127 114.630 1163 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.47 % Allowed : 28.36 % Favored : 69.17 % 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: 1.52 (0.27), residues: 1068 helix: 1.91 (0.25), residues: 433 sheet: 0.09 (0.37), residues: 201 loop : 0.70 (0.33), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 70 TYR 0.020 0.002 TYR C 87 PHE 0.019 0.001 PHE D 66 TRP 0.008 0.001 TRP B 217 HIS 0.003 0.000 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 8711) covalent geometry : angle 0.57401 / 0.28 (11775) SS BOND : bond 0.00544 / 0.34 ( 1) SS BOND : angle 0.53292 / 0.24 ( 2) hydrogen bonds : bond 0.03385 / 2.29 ( 411) hydrogen bonds : angle 4.60114 / 3.25 ( 1206) metal coordination : bond 0.00554 / 0.30 ( 4) metal coordination : angle 2.58216 / 0.97 ( 6) Misc. bond : bond 0.00003 / 0.00 ( 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 120 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.8064 (mtm-85) REVERT: B 97 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8474 (mtm) REVERT: B 522 PHE cc_start: 0.6146 (m-80) cc_final: 0.5900 (m-10) REVERT: C 62 MET cc_start: 0.8963 (mtt) cc_final: 0.8727 (mtt) REVERT: C 122 GLU cc_start: 0.7948 (pp20) cc_final: 0.7539 (pp20) REVERT: D 46 LYS cc_start: 0.8375 (mmtm) cc_final: 0.8025 (mptt) REVERT: D 59 MET cc_start: 0.7510 (pmm) cc_final: 0.6647 (ppp) REVERT: D 60 ASN cc_start: 0.8565 (t0) cc_final: 0.8247 (t0) REVERT: D 67 GLU cc_start: 0.8952 (mp0) cc_final: 0.8748 (mp0) outliers start: 23 outliers final: 11 residues processed: 114 average time/residue: 0.4835 time to fit residues: 58.7553 Evaluate side-chains 107 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 90 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 0.0050 chunk 42 optimal weight: 4.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3180 r_free = 0.3180 target = 0.083008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.058719 restraints weight = 16003.993| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.37 r_work: 0.2632 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1931 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= 0.114 Angle : 0.574 10.662 11783 Z= 0.278 Chirality : 0.041 0.162 1306 Planarity : 0.004 0.050 1531 Dihedral : 6.094 113.302 1163 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.15 % Allowed : 28.89 % 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: 1.43 (0.27), residues: 1068 helix: 1.80 (0.25), residues: 441 sheet: 0.12 (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 D 70 TYR 0.020 0.001 TYR C 87 PHE 0.016 0.001 PHE D 66 TRP 0.007 0.001 TRP A 26 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 8711) covalent geometry : angle 0.57088 / 0.28 (11775) SS BOND : bond 0.00363 / 0.23 ( 1) SS BOND : angle 0.67722 / 0.32 ( 2) hydrogen bonds : bond 0.03239 / 2.19 ( 411) hydrogen bonds : angle 4.55612 / 3.22 ( 1206) metal coordination : bond 0.00497 / 0.27 ( 4) metal coordination : angle 2.50910 / 0.93 ( 6) Misc. bond : bond 0.00000 / 0.00 ( 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 119 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8303 (mtm-85) cc_final: 0.8101 (mtm-85) REVERT: B 168 ARG cc_start: 0.8403 (tpt-90) cc_final: 0.8189 (tpp80) REVERT: B 522 PHE cc_start: 0.6192 (m-80) cc_final: 0.5946 (m-10) REVERT: C 62 MET cc_start: 0.8977 (mtt) cc_final: 0.8692 (mtt) REVERT: C 122 GLU cc_start: 0.7929 (pp20) cc_final: 0.7538 (pp20) REVERT: D 40 MET cc_start: 0.8350 (mmm) cc_final: 0.7703 (mpt) REVERT: D 46 LYS cc_start: 0.8343 (mmtm) cc_final: 0.8106 (mptt) REVERT: D 59 MET cc_start: 0.7533 (pmm) cc_final: 0.6702 (ppp) REVERT: D 60 ASN cc_start: 0.8489 (t0) cc_final: 0.8172 (t0) REVERT: D 67 GLU cc_start: 0.8910 (mp0) cc_final: 0.8670 (mp0) REVERT: D 78 LYS cc_start: 0.9182 (mmpt) cc_final: 0.8793 (mmpt) outliers start: 20 outliers final: 10 residues processed: 115 average time/residue: 0.4615 time to fit residues: 56.7590 Evaluate side-chains 107 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 ASN ** B 382 ASN ** 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 = 0.3179 r_free = 0.3179 target = 0.082949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.058703 restraints weight = 16289.359| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.39 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: 0.8243 moved from start: 0.2020 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= 0.124 Angle : 0.567 8.372 11783 Z= 0.277 Chirality : 0.041 0.155 1306 Planarity : 0.004 0.051 1531 Dihedral : 6.054 112.276 1163 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.83 % Allowed : 29.43 % 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: 1.44 (0.27), residues: 1068 helix: 1.82 (0.25), residues: 441 sheet: 0.10 (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 D 70 TYR 0.022 0.001 TYR A 262 PHE 0.011 0.001 PHE D 66 TRP 0.008 0.001 TRP B 217 HIS 0.001 0.000 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 8711) covalent geometry : angle 0.56382 / 0.28 (11775) SS BOND : bond 0.00311 / 0.19 ( 1) SS BOND : angle 0.57292 / 0.27 ( 2) hydrogen bonds : bond 0.03273 / 2.21 ( 411) hydrogen bonds : angle 4.50573 / 3.18 ( 1206) metal coordination : bond 0.00586 / 0.31 ( 4) metal coordination : angle 2.56422 / 0.95 ( 6) Misc. bond : bond 0.00005 / 0.00 ( 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 119 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 ARG cc_start: 0.8445 (tpt-90) cc_final: 0.8221 (tpp80) REVERT: B 522 PHE cc_start: 0.6480 (m-80) cc_final: 0.6213 (m-80) REVERT: C 62 MET cc_start: 0.8960 (mtt) cc_final: 0.8707 (mtt) REVERT: C 122 GLU cc_start: 0.7952 (pp20) cc_final: 0.7572 (pp20) REVERT: D 23 LYS cc_start: 0.7895 (tppp) cc_final: 0.7648 (tppp) REVERT: D 39 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8210 (mmmt) REVERT: D 40 MET cc_start: 0.8221 (mmm) cc_final: 0.7631 (mpm) REVERT: D 46 LYS cc_start: 0.8313 (mmtm) cc_final: 0.8058 (mptt) REVERT: D 59 MET cc_start: 0.7575 (pmm) cc_final: 0.6781 (ppp) REVERT: D 60 ASN cc_start: 0.8490 (t0) cc_final: 0.8172 (t0) outliers start: 17 outliers final: 13 residues processed: 116 average time/residue: 0.5114 time to fit residues: 63.2992 Evaluate side-chains 111 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 81 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 0.0570 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.084958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.060783 restraints weight = 15788.689| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.36 r_work: 0.2646 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2081 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= 0.115 Angle : 0.574 10.344 11783 Z= 0.277 Chirality : 0.041 0.146 1306 Planarity : 0.004 0.051 1531 Dihedral : 6.046 111.258 1163 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.93 % Allowed : 29.97 % Favored : 68.10 % 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: 1.82 (0.25), residues: 441 sheet: 0.10 (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 D 70 TYR 0.020 0.001 TYR C 87 PHE 0.013 0.001 PHE D 36 TRP 0.008 0.001 TRP B 217 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 ( 8711) covalent geometry : angle 0.57140 / 0.28 (11775) SS BOND : bond 0.00312 / 0.19 ( 1) SS BOND : angle 0.58374 / 0.28 ( 2) hydrogen bonds : bond 0.03209 / 2.16 ( 411) hydrogen bonds : angle 4.50927 / 3.19 ( 1206) metal coordination : bond 0.00498 / 0.27 ( 4) metal coordination : angle 2.45006 / 0.91 ( 6) Misc. bond : bond 0.00002 / 0.00 ( 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 116 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 168 ARG cc_start: 0.8475 (tpt-90) cc_final: 0.8211 (tpp80) REVERT: B 522 PHE cc_start: 0.6470 (m-80) cc_final: 0.6075 (m-10) REVERT: C 62 MET cc_start: 0.8957 (mtt) cc_final: 0.8663 (mtt) REVERT: C 122 GLU cc_start: 0.7949 (pp20) cc_final: 0.7571 (pp20) REVERT: D 46 LYS cc_start: 0.8330 (mmtm) cc_final: 0.8071 (mptt) REVERT: D 59 MET cc_start: 0.7571 (pmm) cc_final: 0.6756 (ppp) REVERT: D 60 ASN cc_start: 0.8480 (t0) cc_final: 0.8158 (t0) REVERT: D 67 GLU cc_start: 0.8843 (mp0) cc_final: 0.8501 (mp0) outliers start: 18 outliers final: 15 residues processed: 113 average time/residue: 0.4637 time to fit residues: 55.9839 Evaluate side-chains 111 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 164 TYR 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 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 66 ASP 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: 1.9990 chunk 24 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 92 optimal weight: 0.0980 chunk 57 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 ASN ** B 382 ASN ** 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 = 0.3161 r_free = 0.3161 target = 0.081979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.058202 restraints weight = 16526.103| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.37 r_work: 0.2600 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2123 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= 0.130 Angle : 0.593 11.364 11783 Z= 0.284 Chirality : 0.041 0.161 1306 Planarity : 0.004 0.048 1531 Dihedral : 6.033 110.923 1163 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.93 % Allowed : 29.97 % Favored : 68.10 % 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: 1.84 (0.25), residues: 441 sheet: 0.11 (0.38), residues: 201 loop : 0.70 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 59 TYR 0.020 0.001 TYR C 87 PHE 0.012 0.001 PHE D 36 TRP 0.008 0.001 TRP B 217 HIS 0.001 0.000 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8711) covalent geometry : angle 0.59074 / 0.28 (11775) SS BOND : bond 0.00316 / 0.20 ( 1) SS BOND : angle 0.61476 / 0.29 ( 2) hydrogen bonds : bond 0.03254 / 2.20 ( 411) hydrogen bonds : angle 4.50940 / 3.19 ( 1206) metal coordination : bond 0.00602 / 0.32 ( 4) metal coordination : angle 2.50173 / 0.92 ( 6) Misc. bond : bond 0.00006 / 0.00 ( 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 115 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 168 ARG cc_start: 0.8455 (tpt-90) cc_final: 0.8190 (tpp80) REVERT: B 522 PHE cc_start: 0.6600 (m-80) cc_final: 0.6331 (m-80) REVERT: C 62 MET cc_start: 0.8946 (mtt) cc_final: 0.8692 (mtt) REVERT: C 122 GLU cc_start: 0.8021 (pp20) cc_final: 0.7641 (pp20) REVERT: D 40 MET cc_start: 0.8206 (mmm) cc_final: 0.7388 (mpt) REVERT: D 46 LYS cc_start: 0.8346 (mmtm) cc_final: 0.8075 (mptt) REVERT: D 59 MET cc_start: 0.7636 (pmm) cc_final: 0.6800 (ppp) REVERT: D 67 GLU cc_start: 0.8833 (mp0) cc_final: 0.8484 (mp0) outliers start: 18 outliers final: 15 residues processed: 111 average time/residue: 0.4840 time to fit residues: 57.4375 Evaluate side-chains 111 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 212 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 355 VAL 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 41 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** 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 = 0.3158 r_free = 0.3158 target = 0.081777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.058189 restraints weight = 16485.338| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.34 r_work: 0.2595 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2123 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= 0.135 Angle : 0.593 11.862 11783 Z= 0.285 Chirality : 0.041 0.140 1306 Planarity : 0.004 0.047 1531 Dihedral : 6.037 110.660 1163 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.61 % Allowed : 30.18 % 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: 1.84 (0.25), residues: 441 sheet: 0.10 (0.38), residues: 201 loop : 0.70 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 235 TYR 0.020 0.001 TYR B 265 PHE 0.014 0.001 PHE D 36 TRP 0.008 0.001 TRP B 217 HIS 0.006 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 8711) covalent geometry : angle 0.59064 / 0.29 (11775) SS BOND : bond 0.00318 / 0.20 ( 1) SS BOND : angle 0.61262 / 0.29 ( 2) hydrogen bonds : bond 0.03277 / 2.21 ( 411) hydrogen bonds : angle 4.49161 / 3.17 ( 1206) metal coordination : bond 0.00682 / 0.37 ( 4) metal coordination : angle 2.57036 / 0.95 ( 6) Misc. bond : bond 0.00007 / 0.00 ( 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 112 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 168 ARG cc_start: 0.8461 (tpt-90) cc_final: 0.8176 (tpp80) REVERT: C 54 GLU cc_start: 0.8300 (pt0) cc_final: 0.7771 (pm20) REVERT: C 122 GLU cc_start: 0.8032 (pp20) cc_final: 0.7649 (pp20) REVERT: D 40 MET cc_start: 0.8205 (mmm) cc_final: 0.7405 (mpt) REVERT: D 46 LYS cc_start: 0.8341 (mmtm) cc_final: 0.8070 (mptt) REVERT: D 59 MET cc_start: 0.7631 (pmm) cc_final: 0.6940 (ppp) REVERT: D 60 ASN cc_start: 0.8417 (t0) cc_final: 0.8110 (t0) REVERT: D 67 GLU cc_start: 0.8816 (mp0) cc_final: 0.8467 (mp0) outliers start: 15 outliers final: 15 residues processed: 111 average time/residue: 0.5091 time to fit residues: 60.2916 Evaluate side-chains 110 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 355 VAL 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: 0.2980 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN B 58 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.081604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.057901 restraints weight = 16558.963| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.36 r_work: 0.2589 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8717 Z= 0.141 Angle : 0.600 11.812 11783 Z= 0.287 Chirality : 0.041 0.139 1306 Planarity : 0.004 0.047 1531 Dihedral : 6.044 110.480 1163 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.72 % Allowed : 30.29 % 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: 1.48 (0.27), residues: 1068 helix: 1.84 (0.25), residues: 441 sheet: 0.08 (0.38), residues: 201 loop : 0.70 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 235 TYR 0.021 0.002 TYR C 87 PHE 0.011 0.001 PHE B 83 TRP 0.008 0.001 TRP B 217 HIS 0.005 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 8711) covalent geometry : angle 0.59775 / 0.29 (11775) SS BOND : bond 0.00320 / 0.20 ( 1) SS BOND : angle 0.61394 / 0.29 ( 2) hydrogen bonds : bond 0.03303 / 2.23 ( 411) hydrogen bonds : angle 4.48330 / 3.16 ( 1206) metal coordination : bond 0.00702 / 0.38 ( 4) metal coordination : angle 2.58641 / 0.96 ( 6) Misc. bond : bond 0.00010 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2286.86 seconds wall clock time: 39 minutes 39.40 seconds (2379.40 seconds total)