Starting phenix.real_space_refine on Tue Apr 9 21:28:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjp_33233/04_2024/7xjp_33233_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjp_33233/04_2024/7xjp_33233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjp_33233/04_2024/7xjp_33233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjp_33233/04_2024/7xjp_33233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjp_33233/04_2024/7xjp_33233_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjp_33233/04_2024/7xjp_33233_updated.pdb" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8627 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 39 5.16 5 C 5693 2.51 5 N 1518 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 201": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 499": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8930 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4720 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 21, 'TRANS': 558} Chain breaks: 1 Chain: "B" Number of atoms: 4140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4140 Classifications: {'peptide': 509} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 492} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'APR': 1, 'IPA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.58, per 1000 atoms: 0.62 Number of scatterers: 8930 At special positions: 0 Unit cell: (84.435, 122.322, 97.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 5 15.00 O 1675 8.00 N 1518 7.00 C 5693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 1.7 seconds 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 3 sheets defined 57.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 11 through 25 removed outlier: 3.780A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 103 through 112 Processing helix chain 'A' and resid 123 through 139 removed outlier: 3.652A pdb=" N ALA A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 189 through 194 removed outlier: 4.602A pdb=" N MET A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 194' Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 222 through 245 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.861A pdb=" N PHE A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.732A pdb=" N PHE A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.894A pdb=" N SER A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE A 309 " --> pdb=" O TRP A 306 " (cutoff:3.500A) Proline residue: A 310 - end of helix Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'A' and resid 352 through 379 Processing helix chain 'A' and resid 382 through 393 removed outlier: 3.931A pdb=" N ILE A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 401 Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 416 through 441 Processing helix chain 'A' and resid 447 through 450 No H-bonds generated for 'chain 'A' and resid 447 through 450' Processing helix chain 'A' and resid 453 through 475 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 485 through 488 No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 492 through 505 Processing helix chain 'A' and resid 548 through 555 removed outlier: 3.552A pdb=" N GLU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 580 removed outlier: 6.311A pdb=" N VAL A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ARG A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 588 No H-bonds generated for 'chain 'A' and resid 585 through 588' Processing helix chain 'A' and resid 594 through 601 removed outlier: 3.926A pdb=" N THR A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'B' and resid 4 through 19 Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 110 through 135 removed outlier: 4.913A pdb=" N THR B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 160 Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.756A pdb=" N LEU B 263 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 316 removed outlier: 4.073A pdb=" N MET B 293 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 373 through 395 Proline residue: B 387 - end of helix Processing helix chain 'B' and resid 401 through 404 No H-bonds generated for 'chain 'B' and resid 401 through 404' Processing helix chain 'B' and resid 408 through 421 removed outlier: 3.795A pdb=" N GLU B 420 " --> pdb=" O TRP B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 460 Processing helix chain 'B' and resid 467 through 488 Processing helix chain 'B' and resid 494 through 497 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 520 through 526 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 35 removed outlier: 6.183A pdb=" N GLN A 116 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE A 41 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A 118 " --> pdb=" O PHE A 41 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N PHE A 43 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR A 120 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG A 152 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N GLY A 121 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 154 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR A 272 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL A 183 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL A 274 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU A 331 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ALA A 283 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN A 333 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 63 through 65 Processing sheet with id= C, first strand: chain 'B' and resid 56 through 61 removed outlier: 8.630A pdb=" N VAL B 68 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 141 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N PHE B 70 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR B 143 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU B 171 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY B 144 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 173 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR B 218 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL B 202 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 220 " --> pdb=" O VAL B 202 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2726 1.34 - 1.45: 1418 1.45 - 1.57: 4918 1.57 - 1.69: 9 1.69 - 1.81: 61 Bond restraints: 9132 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.05e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.59e+01 bond pdb=" C8 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.21e+01 bond pdb=" C5 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.387 1.342 0.045 1.00e-02 1.00e+04 1.98e+01 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.333 0.041 1.00e-02 1.00e+04 1.70e+01 ... (remaining 9127 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.98: 174 105.98 - 113.48: 5044 113.48 - 120.98: 4787 120.98 - 128.48: 2244 128.48 - 135.98: 75 Bond angle restraints: 12324 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 121.89 17.98 1.00e+00 1.00e+00 3.23e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 122.91 13.92 1.00e+00 1.00e+00 1.94e+02 angle pdb=" C5 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 126.80 118.66 8.14 1.00e+00 1.00e+00 6.63e+01 angle pdb=" N3 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 127.04 135.04 -8.00 1.15e+00 7.59e-01 4.85e+01 angle pdb=" N1 ATP B 601 " pdb=" C2 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 128.69 123.63 5.06 1.00e+00 1.00e+00 2.56e+01 ... (remaining 12319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5013 17.43 - 34.85: 431 34.85 - 52.28: 87 52.28 - 69.70: 7 69.70 - 87.13: 8 Dihedral angle restraints: 5546 sinusoidal: 2351 harmonic: 3195 Sorted by residual: dihedral pdb=" CA HIS A 122 " pdb=" C HIS A 122 " pdb=" N SER A 123 " pdb=" CA SER A 123 " ideal model delta harmonic sigma weight residual -180.00 -158.29 -21.71 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA LEU A 464 " pdb=" C LEU A 464 " pdb=" N VAL A 465 " pdb=" CA VAL A 465 " ideal model delta harmonic sigma weight residual 180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ARG A 280 " pdb=" C ARG A 280 " pdb=" N LEU A 281 " pdb=" CA LEU A 281 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 944 0.045 - 0.090: 283 0.090 - 0.134: 81 0.134 - 0.179: 17 0.179 - 0.224: 9 Chirality restraints: 1334 Sorted by residual: chirality pdb=" CA LEU B 370 " pdb=" N LEU B 370 " pdb=" C LEU B 370 " pdb=" CB LEU B 370 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE B 369 " pdb=" N ILE B 369 " pdb=" C ILE B 369 " pdb=" CB ILE B 369 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE A 578 " pdb=" N ILE A 578 " pdb=" C ILE A 578 " pdb=" CB ILE A 578 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1331 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 573 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.78e+00 pdb=" C MET A 573 " -0.045 2.00e-02 2.50e+03 pdb=" O MET A 573 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 574 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 189 " -0.030 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 190 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 190 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 190 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 386 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.84e+00 pdb=" N PRO B 387 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 387 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 387 " 0.024 5.00e-02 4.00e+02 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1350 2.75 - 3.29: 9278 3.29 - 3.83: 15163 3.83 - 4.36: 18348 4.36 - 4.90: 30001 Nonbonded interactions: 74140 Sorted by model distance: nonbonded pdb=" OD2 ASP A 187 " pdb=" OH TYR A 320 " model vdw 2.215 2.440 nonbonded pdb=" O SER B 80 " pdb=" NE2 HIS B 109 " model vdw 2.250 2.520 nonbonded pdb=" O ILE B 75 " pdb=" NH1 ARG B 77 " model vdw 2.256 2.520 nonbonded pdb=" NE1 TRP B 26 " pdb=" OG SER B 252 " model vdw 2.256 2.520 nonbonded pdb=" O THR B 133 " pdb=" OG SER B 136 " model vdw 2.258 2.440 ... (remaining 74135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 4.130 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.390 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 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 : 0.005 0.081 9132 Z= 0.338 Angle : 0.799 17.982 12324 Z= 0.549 Chirality : 0.050 0.224 1334 Planarity : 0.004 0.045 1557 Dihedral : 13.661 87.126 3474 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 0.82 % Allowed : 1.84 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.23), residues: 1079 helix: -0.73 (0.19), residues: 633 sheet: -1.72 (0.48), residues: 100 loop : -1.64 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 507 HIS 0.004 0.001 HIS A 474 PHE 0.013 0.001 PHE B 444 TYR 0.013 0.001 TYR A 30 ARG 0.004 0.000 ARG A 596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 181 average time/residue: 1.4054 time to fit residues: 269.5352 Evaluate side-chains 104 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 523 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS B 103 ASN B 200 HIS ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 287 ASN B 342 ASN B 349 ASN B 517 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9132 Z= 0.264 Angle : 0.592 6.878 12324 Z= 0.307 Chirality : 0.042 0.168 1334 Planarity : 0.004 0.047 1557 Dihedral : 7.941 85.983 1273 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.95 % Allowed : 13.42 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1079 helix: 0.49 (0.20), residues: 626 sheet: -1.36 (0.50), residues: 99 loop : -1.07 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 577 HIS 0.005 0.001 HIS A 31 PHE 0.012 0.001 PHE B 444 TYR 0.015 0.002 TYR A 560 ARG 0.006 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ARG cc_start: 0.4498 (OUTLIER) cc_final: 0.3593 (tpt-90) REVERT: B 369 ILE cc_start: 0.5559 (mm) cc_final: 0.5303 (mm) outliers start: 19 outliers final: 7 residues processed: 123 average time/residue: 1.3116 time to fit residues: 171.9737 Evaluate side-chains 93 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.0670 chunk 81 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 0.3980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN A 381 GLN A 606 HIS B 187 GLN B 200 HIS B 349 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9132 Z= 0.158 Angle : 0.542 7.073 12324 Z= 0.280 Chirality : 0.039 0.172 1334 Planarity : 0.004 0.042 1557 Dihedral : 7.360 70.723 1268 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.13 % Allowed : 15.88 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1079 helix: 0.87 (0.21), residues: 629 sheet: -0.88 (0.53), residues: 100 loop : -0.75 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 577 HIS 0.005 0.001 HIS B 200 PHE 0.009 0.001 PHE B 97 TYR 0.021 0.001 TYR A 560 ARG 0.008 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ARG cc_start: 0.4514 (OUTLIER) cc_final: 0.3619 (tpt-90) outliers start: 11 outliers final: 4 residues processed: 106 average time/residue: 1.2747 time to fit residues: 144.6673 Evaluate side-chains 86 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 0.1980 chunk 50 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 104 optimal weight: 0.0570 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 ASN A 606 HIS B 187 GLN B 349 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9132 Z= 0.156 Angle : 0.538 7.040 12324 Z= 0.276 Chirality : 0.039 0.214 1334 Planarity : 0.004 0.040 1557 Dihedral : 6.852 74.901 1268 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.95 % Allowed : 15.98 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1079 helix: 1.20 (0.21), residues: 618 sheet: -0.57 (0.54), residues: 100 loop : -0.67 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 598 HIS 0.003 0.001 HIS B 408 PHE 0.014 0.001 PHE B 97 TYR 0.026 0.001 TYR B 310 ARG 0.006 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 269 ARG cc_start: 0.4541 (OUTLIER) cc_final: 0.3647 (tpt-90) REVERT: B 431 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6575 (mmtt) outliers start: 19 outliers final: 4 residues processed: 107 average time/residue: 1.3399 time to fit residues: 153.2381 Evaluate side-chains 86 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 431 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 0.1980 chunk 0 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS B 187 GLN B 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9132 Z= 0.170 Angle : 0.556 8.398 12324 Z= 0.285 Chirality : 0.039 0.179 1334 Planarity : 0.004 0.039 1557 Dihedral : 6.610 76.810 1268 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.95 % Allowed : 17.52 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1079 helix: 1.27 (0.21), residues: 619 sheet: -0.43 (0.55), residues: 100 loop : -0.58 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 598 HIS 0.003 0.001 HIS A 606 PHE 0.017 0.001 PHE B 97 TYR 0.024 0.001 TYR A 560 ARG 0.013 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ARG cc_start: 0.4709 (OUTLIER) cc_final: 0.3698 (tpt-90) REVERT: B 431 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6571 (mmtt) outliers start: 19 outliers final: 8 residues processed: 105 average time/residue: 1.2157 time to fit residues: 137.2283 Evaluate side-chains 92 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 431 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS B 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9132 Z= 0.174 Angle : 0.551 7.172 12324 Z= 0.282 Chirality : 0.039 0.165 1334 Planarity : 0.004 0.039 1557 Dihedral : 6.556 79.816 1268 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.95 % Allowed : 18.34 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1079 helix: 1.36 (0.21), residues: 617 sheet: -0.36 (0.55), residues: 100 loop : -0.53 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 598 HIS 0.002 0.001 HIS A 474 PHE 0.019 0.001 PHE B 97 TYR 0.027 0.001 TYR B 310 ARG 0.008 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ARG cc_start: 0.4881 (OUTLIER) cc_final: 0.3800 (tpt-90) REVERT: B 369 ILE cc_start: 0.5252 (mm) cc_final: 0.5041 (mm) REVERT: B 431 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6593 (mmtt) outliers start: 19 outliers final: 11 residues processed: 111 average time/residue: 1.2633 time to fit residues: 150.0617 Evaluate side-chains 95 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 431 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 0.0670 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS B 103 ASN B 349 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9132 Z= 0.193 Angle : 0.591 12.790 12324 Z= 0.299 Chirality : 0.040 0.154 1334 Planarity : 0.004 0.039 1557 Dihedral : 6.571 80.680 1268 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.74 % Allowed : 19.36 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1079 helix: 1.31 (0.21), residues: 626 sheet: -0.29 (0.56), residues: 100 loop : -0.59 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 598 HIS 0.003 0.001 HIS A 31 PHE 0.020 0.001 PHE B 97 TYR 0.013 0.001 TYR A 560 ARG 0.010 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ARG cc_start: 0.4850 (OUTLIER) cc_final: 0.3730 (tpt-90) REVERT: B 369 ILE cc_start: 0.5396 (mm) cc_final: 0.5136 (mm) REVERT: B 431 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6606 (mmtt) outliers start: 17 outliers final: 13 residues processed: 99 average time/residue: 1.2073 time to fit residues: 128.5243 Evaluate side-chains 97 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 431 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.0370 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 0.0020 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 overall best weight: 0.5066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS B 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9132 Z= 0.166 Angle : 0.581 12.984 12324 Z= 0.294 Chirality : 0.039 0.147 1334 Planarity : 0.004 0.039 1557 Dihedral : 6.435 82.084 1268 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.43 % Allowed : 19.67 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1079 helix: 1.33 (0.21), residues: 626 sheet: -0.20 (0.55), residues: 100 loop : -0.55 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 598 HIS 0.003 0.001 HIS A 31 PHE 0.022 0.001 PHE B 97 TYR 0.012 0.001 TYR A 406 ARG 0.012 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ARG cc_start: 0.4973 (OUTLIER) cc_final: 0.3816 (tpt-90) REVERT: B 369 ILE cc_start: 0.5241 (mm) cc_final: 0.5034 (mm) REVERT: B 431 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6594 (mmtt) outliers start: 14 outliers final: 9 residues processed: 100 average time/residue: 1.2890 time to fit residues: 138.1142 Evaluate side-chains 91 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 431 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS B 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9132 Z= 0.186 Angle : 0.595 13.352 12324 Z= 0.301 Chirality : 0.039 0.147 1334 Planarity : 0.004 0.039 1557 Dihedral : 6.448 82.449 1268 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.54 % Allowed : 19.77 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1079 helix: 1.30 (0.21), residues: 627 sheet: -0.18 (0.55), residues: 100 loop : -0.51 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 598 HIS 0.004 0.001 HIS A 31 PHE 0.023 0.001 PHE B 97 TYR 0.028 0.001 TYR B 310 ARG 0.011 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ARG cc_start: 0.4887 (OUTLIER) cc_final: 0.3774 (tpt-90) REVERT: B 431 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6622 (mmtt) outliers start: 15 outliers final: 13 residues processed: 92 average time/residue: 1.1432 time to fit residues: 113.3787 Evaluate side-chains 95 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 431 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS B 103 ASN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9132 Z= 0.217 Angle : 0.626 13.714 12324 Z= 0.316 Chirality : 0.041 0.241 1334 Planarity : 0.004 0.038 1557 Dihedral : 6.409 83.399 1268 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.64 % Allowed : 19.98 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1079 helix: 1.30 (0.21), residues: 627 sheet: -0.24 (0.55), residues: 100 loop : -0.47 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 598 HIS 0.004 0.001 HIS A 31 PHE 0.025 0.001 PHE B 97 TYR 0.014 0.001 TYR A 560 ARG 0.015 0.000 ARG A 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ARG cc_start: 0.4965 (OUTLIER) cc_final: 0.3868 (tpt-90) REVERT: B 431 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6640 (mmtt) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 1.1914 time to fit residues: 123.0693 Evaluate side-chains 93 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 431 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS B 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.123638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.101722 restraints weight = 18130.060| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 3.30 r_work: 0.3704 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9132 Z= 0.200 Angle : 0.622 13.622 12324 Z= 0.315 Chirality : 0.040 0.220 1334 Planarity : 0.004 0.039 1557 Dihedral : 6.160 84.550 1268 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.74 % Allowed : 20.18 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1079 helix: 1.32 (0.21), residues: 623 sheet: -0.17 (0.56), residues: 100 loop : -0.50 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 598 HIS 0.004 0.001 HIS A 31 PHE 0.024 0.001 PHE B 97 TYR 0.031 0.002 TYR B 310 ARG 0.011 0.000 ARG A 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.58 seconds wall clock time: 61 minutes 5.67 seconds (3665.67 seconds total)