Starting phenix.real_space_refine on Thu Feb 15 01:58:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrm_14919/02_2024/7zrm_14919_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrm_14919/02_2024/7zrm_14919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrm_14919/02_2024/7zrm_14919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrm_14919/02_2024/7zrm_14919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrm_14919/02_2024/7zrm_14919_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrm_14919/02_2024/7zrm_14919_updated.pdb" } resolution = 3.7 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= 0.007 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: 7 Type Number sf(0) Gaussians K 5 8.98 5 P 3 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6971 2.51 5 N 1826 2.21 5 O 1971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10839 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5020 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 26, 'TRANS': 649} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.50, per 1000 atoms: 0.60 Number of scatterers: 10839 At special positions: 0 Unit cell: (94.116, 110.308, 149.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 5 19.00 S 62 16.00 P 3 15.00 Mg 1 11.99 O 1971 8.00 N 1826 7.00 C 6971 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=0, symmetry=0 Time building additional restraints: 4.82 Conformation dependent library (CDL) restraints added in 2.3 seconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 7 sheets defined 55.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 Proline residue: A 22 - end of helix removed outlier: 3.986A pdb=" N SER A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 134 through 156 Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 178 through 192 Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.893A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.528A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 278 through 304 removed outlier: 4.067A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 356 through 367 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 378 through 398 Processing helix chain 'A' and resid 411 through 436 removed outlier: 4.588A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 439 through 444 removed outlier: 4.136A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 479 through 508 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 524 through 541 Processing helix chain 'A' and resid 544 through 549 Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'C' and resid 4 through 20 removed outlier: 3.715A pdb=" N THR C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 118 through 121 No H-bonds generated for 'chain 'C' and resid 118 through 121' Processing helix chain 'C' and resid 134 through 147 Proline residue: C 142 - end of helix Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'D' and resid 3 through 24 Processing helix chain 'B' and resid 12 through 24 removed outlier: 4.590A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 54 removed outlier: 3.522A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 96 Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 199 through 206 Processing helix chain 'B' and resid 216 through 246 removed outlier: 3.844A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 285 removed outlier: 5.823A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 removed outlier: 3.603A pdb=" N ALA B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.843A pdb=" N ALA B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'B' and resid 398 through 408 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 453 through 463 Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 496 through 508 removed outlier: 4.105A pdb=" N LEU B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 528 Proline residue: B 524 - end of helix Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 558 through 594 removed outlier: 4.097A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.838A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 637 removed outlier: 3.868A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 646 through 657 Processing helix chain 'B' and resid 659 through 679 Proline residue: B 665 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.915A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.542A pdb=" N VAL B 134 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 150 through 153 removed outlier: 3.620A pdb=" N ALA B 151 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL B 165 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 287 through 289 Processing sheet with id= F, first strand: chain 'B' and resid 466 through 469 removed outlier: 6.476A pdb=" N VAL B 531 " --> pdb=" O MET B 515 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N GLY B 517 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 533 " --> pdb=" O GLY B 517 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 383 through 385 555 hydrogen bonds defined for protein. 1650 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: 2.95 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1767 1.32 - 1.44: 2731 1.44 - 1.57: 6421 1.57 - 1.70: 4 1.70 - 1.82: 112 Bond restraints: 11035 Sorted by residual: bond pdb=" OD1 PHD B 307 " pdb=" P PHD B 307 " ideal model delta sigma weight residual 1.816 1.593 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C ASN B 26 " pdb=" N PRO B 27 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.57e+00 bond pdb=" CG PHD B 307 " pdb=" OD1 PHD B 307 " ideal model delta sigma weight residual 1.300 1.330 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" SD MET A 489 " pdb=" CE MET A 489 " ideal model delta sigma weight residual 1.791 1.754 0.037 2.50e-02 1.60e+03 2.17e+00 bond pdb=" CB PRO B 164 " pdb=" CG PRO B 164 " ideal model delta sigma weight residual 1.492 1.561 -0.069 5.00e-02 4.00e+02 1.93e+00 ... (remaining 11030 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.92: 351 106.92 - 114.21: 6504 114.21 - 121.51: 5639 121.51 - 128.80: 2460 128.80 - 136.10: 72 Bond angle restraints: 15026 Sorted by residual: angle pdb=" C GLY A 374 " pdb=" N GLY A 375 " pdb=" CA GLY A 375 " ideal model delta sigma weight residual 121.41 130.73 -9.32 1.96e+00 2.60e-01 2.26e+01 angle pdb=" CB MET A 501 " pdb=" CG MET A 501 " pdb=" SD MET A 501 " ideal model delta sigma weight residual 112.70 124.35 -11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C PHE A 471 " pdb=" N ALA A 472 " pdb=" CA ALA A 472 " ideal model delta sigma weight residual 121.54 128.79 -7.25 1.91e+00 2.74e-01 1.44e+01 angle pdb=" CA TYR A 381 " pdb=" CB TYR A 381 " pdb=" CG TYR A 381 " ideal model delta sigma weight residual 113.90 120.47 -6.57 1.80e+00 3.09e-01 1.33e+01 angle pdb=" C PRO B 27 " pdb=" N GLN B 28 " pdb=" CA GLN B 28 " ideal model delta sigma weight residual 122.08 127.12 -5.04 1.47e+00 4.63e-01 1.17e+01 ... (remaining 15021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.60: 6172 24.60 - 49.19: 345 49.19 - 73.79: 29 73.79 - 98.38: 8 98.38 - 122.98: 1 Dihedral angle restraints: 6555 sinusoidal: 2449 harmonic: 4106 Sorted by residual: dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 62.97 -122.98 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" CA THR A 542 " pdb=" C THR A 542 " pdb=" N PHE A 543 " pdb=" CA PHE A 543 " ideal model delta harmonic sigma weight residual 180.00 -159.34 -20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA GLY A 495 " pdb=" C GLY A 495 " pdb=" N VAL A 496 " pdb=" CA VAL A 496 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 6552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1361 0.051 - 0.101: 365 0.101 - 0.152: 75 0.152 - 0.203: 8 0.203 - 0.253: 2 Chirality restraints: 1811 Sorted by residual: chirality pdb=" CB ILE A 348 " pdb=" CA ILE A 348 " pdb=" CG1 ILE A 348 " pdb=" CG2 ILE A 348 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CG LEU A 77 " pdb=" CB LEU A 77 " pdb=" CD1 LEU A 77 " pdb=" CD2 LEU A 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1808 not shown) Planarity restraints: 1902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 163 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO B 164 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 100 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.69e+00 pdb=" C VAL B 100 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL B 100 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS B 101 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 495 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO B 496 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 496 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 496 " -0.035 5.00e-02 4.00e+02 ... (remaining 1899 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 3422 2.84 - 3.41: 12445 3.41 - 3.99: 21004 3.99 - 4.56: 29367 4.56 - 5.14: 42181 Nonbonded interactions: 108419 Sorted by model distance: nonbonded pdb=" O GLU A 413 " pdb=" OG1 THR A 417 " model vdw 2.260 2.440 nonbonded pdb=" OG SER A 343 " pdb=" O ASN A 466 " model vdw 2.265 2.440 nonbonded pdb=" O SER A 119 " pdb=" OG1 THR A 123 " model vdw 2.265 2.440 nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.294 2.440 nonbonded pdb=" OG1 THR A 113 " pdb=" OD1 ASN A 466 " model vdw 2.305 2.440 ... (remaining 108414 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.620 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.640 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.223 11035 Z= 0.305 Angle : 0.808 11.653 15026 Z= 0.402 Chirality : 0.048 0.253 1811 Planarity : 0.006 0.101 1902 Dihedral : 14.868 122.976 3917 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.35 (0.20), residues: 1439 helix: 0.02 (0.16), residues: 864 sheet: -1.95 (0.59), residues: 74 loop : -2.29 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 176 HIS 0.005 0.001 HIS A 242 PHE 0.023 0.002 PHE A 109 TYR 0.034 0.002 TYR A 381 ARG 0.013 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.234 Fit side-chains REVERT: A 360 MET cc_start: 0.7207 (tmm) cc_final: 0.6960 (tmm) REVERT: C 170 TYR cc_start: 0.6769 (p90) cc_final: 0.6355 (p90) REVERT: D 21 TYR cc_start: 0.7067 (t80) cc_final: 0.6453 (t80) REVERT: B 36 MET cc_start: 0.7431 (mmt) cc_final: 0.7136 (mmt) REVERT: B 74 ILE cc_start: 0.7513 (pt) cc_final: 0.7143 (mt) REVERT: B 101 LYS cc_start: 0.6504 (mtmm) cc_final: 0.6014 (pptt) REVERT: B 332 THR cc_start: 0.6743 (p) cc_final: 0.6405 (t) REVERT: B 383 MET cc_start: 0.5847 (ppp) cc_final: 0.5314 (tpp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2011 time to fit residues: 54.6602 Evaluate side-chains 150 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN A 231 ASN B 459 GLN B 521 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11035 Z= 0.223 Angle : 0.549 6.354 15026 Z= 0.271 Chirality : 0.040 0.160 1811 Planarity : 0.004 0.053 1902 Dihedral : 5.752 109.963 1537 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.06 % Allowed : 9.88 % Favored : 89.07 % 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: -0.51 (0.21), residues: 1439 helix: 0.82 (0.17), residues: 852 sheet: -1.63 (0.66), residues: 60 loop : -2.14 (0.24), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 176 HIS 0.002 0.001 HIS A 351 PHE 0.014 0.001 PHE A 373 TYR 0.026 0.001 TYR A 381 ARG 0.004 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 1.217 Fit side-chains REVERT: A 360 MET cc_start: 0.7287 (tmm) cc_final: 0.7083 (tmm) REVERT: C 170 TYR cc_start: 0.7060 (p90) cc_final: 0.6652 (p90) REVERT: B 203 MET cc_start: 0.6523 (ptt) cc_final: 0.6313 (ptt) REVERT: B 383 MET cc_start: 0.6016 (ppp) cc_final: 0.5445 (tpp) REVERT: B 608 MET cc_start: 0.8208 (mtm) cc_final: 0.7848 (mtm) outliers start: 12 outliers final: 11 residues processed: 163 average time/residue: 0.2017 time to fit residues: 49.2360 Evaluate side-chains 157 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 88 optimal weight: 30.0000 chunk 35 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 44 optimal weight: 0.0870 chunk 104 optimal weight: 2.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 319 ASN ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 521 ASN B 540 GLN B 563 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11035 Z= 0.321 Angle : 0.606 6.878 15026 Z= 0.303 Chirality : 0.042 0.171 1811 Planarity : 0.004 0.052 1902 Dihedral : 5.913 112.002 1537 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.73 % Allowed : 14.20 % Favored : 83.07 % 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: -0.52 (0.22), residues: 1439 helix: 0.86 (0.17), residues: 861 sheet: -1.95 (0.64), residues: 60 loop : -2.25 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 176 HIS 0.004 0.001 HIS A 351 PHE 0.018 0.002 PHE A 373 TYR 0.023 0.002 TYR A 381 ARG 0.005 0.000 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.362 Fit side-chains REVERT: A 114 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.7856 (t0) REVERT: C 130 ASN cc_start: 0.7928 (t0) cc_final: 0.7590 (t0) REVERT: B 36 MET cc_start: 0.7237 (mmt) cc_final: 0.6944 (mmt) REVERT: B 183 LEU cc_start: 0.6079 (mp) cc_final: 0.5000 (tp) REVERT: B 203 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.6398 (ptt) REVERT: B 383 MET cc_start: 0.6362 (ppp) cc_final: 0.5687 (tpp) REVERT: B 411 HIS cc_start: 0.6831 (OUTLIER) cc_final: 0.6629 (t-90) REVERT: B 465 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7726 (mp) REVERT: B 608 MET cc_start: 0.8327 (mtm) cc_final: 0.7963 (mtm) outliers start: 31 outliers final: 18 residues processed: 160 average time/residue: 0.1906 time to fit residues: 47.1705 Evaluate side-chains 154 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 679 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 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 129 GLN A 231 ASN A 367 GLN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11035 Z= 0.177 Angle : 0.526 7.096 15026 Z= 0.259 Chirality : 0.039 0.150 1811 Planarity : 0.004 0.051 1902 Dihedral : 5.597 110.857 1537 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.76 % Allowed : 17.46 % Favored : 80.78 % 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: -0.09 (0.22), residues: 1439 helix: 1.22 (0.18), residues: 855 sheet: -1.83 (0.65), residues: 60 loop : -2.05 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 176 HIS 0.003 0.001 HIS A 242 PHE 0.012 0.001 PHE A 373 TYR 0.025 0.001 TYR A 381 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.170 Fit side-chains REVERT: A 347 VAL cc_start: 0.7586 (m) cc_final: 0.7353 (m) REVERT: C 130 ASN cc_start: 0.7893 (t0) cc_final: 0.7390 (t0) REVERT: B 203 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.6450 (ptt) REVERT: B 383 MET cc_start: 0.6147 (ppp) cc_final: 0.5673 (tpp) REVERT: B 411 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.6673 (t-90) REVERT: B 465 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7595 (mp) outliers start: 20 outliers final: 11 residues processed: 158 average time/residue: 0.2018 time to fit residues: 47.7014 Evaluate side-chains 153 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 5.9990 chunk 78 optimal weight: 0.0040 chunk 2 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 124 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11035 Z= 0.183 Angle : 0.519 6.079 15026 Z= 0.255 Chirality : 0.039 0.148 1811 Planarity : 0.004 0.047 1902 Dihedral : 5.440 109.806 1537 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.03 % Allowed : 17.90 % Favored : 80.07 % 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: 0.01 (0.22), residues: 1439 helix: 1.33 (0.18), residues: 856 sheet: -1.72 (0.66), residues: 60 loop : -2.09 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 186 HIS 0.002 0.001 HIS A 242 PHE 0.012 0.001 PHE A 373 TYR 0.025 0.001 TYR A 381 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.256 Fit side-chains REVERT: C 130 ASN cc_start: 0.7892 (t0) cc_final: 0.7269 (t0) REVERT: B 36 MET cc_start: 0.7254 (mmt) cc_final: 0.7048 (mmt) REVERT: B 203 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6452 (ptt) REVERT: B 383 MET cc_start: 0.6186 (ppp) cc_final: 0.5764 (tpp) REVERT: B 608 MET cc_start: 0.8232 (mtm) cc_final: 0.7852 (mtm) outliers start: 23 outliers final: 16 residues processed: 159 average time/residue: 0.1720 time to fit residues: 42.0049 Evaluate side-chains 153 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 0.0870 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 114 optimal weight: 0.0040 chunk 64 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.7772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11035 Z= 0.157 Angle : 0.510 5.954 15026 Z= 0.250 Chirality : 0.039 0.154 1811 Planarity : 0.004 0.047 1902 Dihedral : 5.295 108.682 1537 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.94 % Allowed : 17.99 % Favored : 80.07 % 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: 0.15 (0.22), residues: 1439 helix: 1.46 (0.18), residues: 853 sheet: -1.71 (0.66), residues: 60 loop : -2.05 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 186 HIS 0.004 0.001 HIS A 451 PHE 0.011 0.001 PHE A 373 TYR 0.024 0.001 TYR A 381 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: C 130 ASN cc_start: 0.7860 (t0) cc_final: 0.7273 (t0) REVERT: B 36 MET cc_start: 0.7342 (mmt) cc_final: 0.7123 (mmt) REVERT: B 186 TRP cc_start: 0.2598 (p-90) cc_final: 0.2236 (p-90) REVERT: B 203 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6447 (ptt) REVERT: B 383 MET cc_start: 0.6158 (ppp) cc_final: 0.5764 (tpp) REVERT: B 608 MET cc_start: 0.8223 (mtm) cc_final: 0.7855 (mtm) outliers start: 22 outliers final: 15 residues processed: 159 average time/residue: 0.1944 time to fit residues: 46.3190 Evaluate side-chains 155 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 116 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11035 Z= 0.332 Angle : 0.602 7.014 15026 Z= 0.300 Chirality : 0.042 0.164 1811 Planarity : 0.004 0.049 1902 Dihedral : 5.597 107.586 1537 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.09 % Allowed : 17.90 % Favored : 79.01 % 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: -0.23 (0.22), residues: 1439 helix: 1.08 (0.18), residues: 862 sheet: -1.69 (0.67), residues: 60 loop : -2.14 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 186 HIS 0.003 0.001 HIS A 351 PHE 0.020 0.002 PHE A 373 TYR 0.020 0.002 TYR A 381 ARG 0.005 0.000 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 1.066 Fit side-chains REVERT: A 366 MET cc_start: 0.8984 (ttm) cc_final: 0.8745 (ttm) REVERT: C 130 ASN cc_start: 0.8062 (t0) cc_final: 0.7649 (t0) REVERT: B 36 MET cc_start: 0.7373 (mmt) cc_final: 0.7089 (mmt) REVERT: B 186 TRP cc_start: 0.2539 (p-90) cc_final: 0.2233 (p-90) REVERT: B 203 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6432 (ptt) REVERT: B 383 MET cc_start: 0.6172 (ppp) cc_final: 0.5644 (tpp) REVERT: B 608 MET cc_start: 0.8203 (mtm) cc_final: 0.7856 (mtm) outliers start: 35 outliers final: 24 residues processed: 161 average time/residue: 0.1829 time to fit residues: 44.9762 Evaluate side-chains 158 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 679 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 87 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11035 Z= 0.164 Angle : 0.536 7.054 15026 Z= 0.265 Chirality : 0.039 0.151 1811 Planarity : 0.004 0.049 1902 Dihedral : 5.396 107.190 1537 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.94 % Allowed : 19.49 % Favored : 78.57 % 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: 0.04 (0.22), residues: 1439 helix: 1.34 (0.18), residues: 859 sheet: -1.63 (0.66), residues: 60 loop : -2.08 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 186 HIS 0.003 0.001 HIS A 242 PHE 0.011 0.001 PHE A 373 TYR 0.026 0.001 TYR A 381 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.236 Fit side-chains REVERT: A 366 MET cc_start: 0.8951 (ttm) cc_final: 0.8662 (ttm) REVERT: C 130 ASN cc_start: 0.7910 (t0) cc_final: 0.7273 (t0) REVERT: B 36 MET cc_start: 0.7384 (mmt) cc_final: 0.7133 (mmt) REVERT: B 203 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6483 (ptt) REVERT: B 383 MET cc_start: 0.6081 (ppp) cc_final: 0.5730 (tpp) REVERT: B 608 MET cc_start: 0.8220 (mtm) cc_final: 0.7877 (mtm) outliers start: 22 outliers final: 17 residues processed: 161 average time/residue: 0.1990 time to fit residues: 48.0321 Evaluate side-chains 156 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 55 optimal weight: 0.0470 chunk 100 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11035 Z= 0.171 Angle : 0.534 6.974 15026 Z= 0.262 Chirality : 0.039 0.155 1811 Planarity : 0.004 0.047 1902 Dihedral : 5.297 106.035 1537 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.03 % Allowed : 19.75 % Favored : 78.22 % 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: 0.07 (0.22), residues: 1439 helix: 1.43 (0.18), residues: 853 sheet: -2.01 (0.60), residues: 70 loop : -2.09 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 186 HIS 0.003 0.001 HIS A 242 PHE 0.013 0.001 PHE A 373 TYR 0.025 0.001 TYR A 381 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.242 Fit side-chains REVERT: A 366 MET cc_start: 0.8943 (ttm) cc_final: 0.8645 (ttm) REVERT: C 130 ASN cc_start: 0.7936 (t0) cc_final: 0.7322 (t0) REVERT: B 36 MET cc_start: 0.7415 (mmt) cc_final: 0.7165 (mmt) REVERT: B 203 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6462 (ptt) REVERT: B 383 MET cc_start: 0.6060 (ppp) cc_final: 0.5740 (tpp) REVERT: B 608 MET cc_start: 0.8159 (mtm) cc_final: 0.7800 (mtm) outliers start: 23 outliers final: 20 residues processed: 156 average time/residue: 0.1685 time to fit residues: 40.1866 Evaluate side-chains 156 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 69 optimal weight: 0.0170 chunk 90 optimal weight: 0.0010 overall best weight: 0.6628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11035 Z= 0.155 Angle : 0.533 6.583 15026 Z= 0.262 Chirality : 0.039 0.152 1811 Planarity : 0.004 0.047 1902 Dihedral : 5.227 105.119 1537 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.85 % Allowed : 20.19 % Favored : 77.95 % 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: 0.17 (0.22), residues: 1439 helix: 1.51 (0.18), residues: 852 sheet: -1.89 (0.60), residues: 70 loop : -2.08 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 186 HIS 0.003 0.001 HIS A 242 PHE 0.011 0.001 PHE A 373 TYR 0.025 0.001 TYR A 381 ARG 0.004 0.000 ARG A 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 142 time to evaluate : 1.163 Fit side-chains REVERT: A 366 MET cc_start: 0.8910 (ttm) cc_final: 0.8648 (ttm) REVERT: A 397 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7759 (mpp) REVERT: C 130 ASN cc_start: 0.7872 (t0) cc_final: 0.7246 (t0) REVERT: B 36 MET cc_start: 0.7401 (mmt) cc_final: 0.7152 (mmt) REVERT: B 203 MET cc_start: 0.6721 (OUTLIER) cc_final: 0.6483 (ptt) REVERT: B 383 MET cc_start: 0.5984 (ppp) cc_final: 0.5732 (tpp) REVERT: B 608 MET cc_start: 0.8117 (mtm) cc_final: 0.7775 (mtm) outliers start: 21 outliers final: 18 residues processed: 157 average time/residue: 0.1910 time to fit residues: 45.7557 Evaluate side-chains 156 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.103826 restraints weight = 17243.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105911 restraints weight = 9226.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.107240 restraints weight = 6276.733| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11035 Z= 0.299 Angle : 0.590 6.382 15026 Z= 0.294 Chirality : 0.041 0.162 1811 Planarity : 0.004 0.047 1902 Dihedral : 5.460 106.250 1537 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.12 % Allowed : 19.75 % Favored : 78.13 % 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: -0.10 (0.22), residues: 1439 helix: 1.22 (0.18), residues: 860 sheet: -1.59 (0.64), residues: 60 loop : -2.16 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 186 HIS 0.003 0.001 HIS A 351 PHE 0.016 0.002 PHE A 373 TYR 0.021 0.002 TYR A 381 ARG 0.004 0.000 ARG B 572 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2028.04 seconds wall clock time: 43 minutes 42.78 seconds (2622.78 seconds total)