Starting phenix.real_space_refine on Tue Mar 3 14:18:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bh9_12187/03_2026/7bh9_12187.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bh9_12187/03_2026/7bh9_12187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bh9_12187/03_2026/7bh9_12187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bh9_12187/03_2026/7bh9_12187.map" model { file = "/net/cci-nas-00/data/ceres_data/7bh9_12187/03_2026/7bh9_12187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bh9_12187/03_2026/7bh9_12187.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 34 5.16 5 C 3787 2.51 5 N 970 2.21 5 O 1084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5876 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4704 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 560} Chain breaks: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 5, 'GLN:plan1': 5, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "E" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1129 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.29, per 1000 atoms: 0.22 Number of scatterers: 5876 At special positions: 0 Unit cell: (68.77, 81.466, 111.09, 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) Zn 1 29.99 S 34 16.00 O 1084 8.00 N 970 7.00 C 3787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=1.99 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 902 " - " ASN A 546 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 53 " Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 262.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1372 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 58.1% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.676A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 81 removed outlier: 3.596A pdb=" N ASN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.009A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 129 removed outlier: 3.507A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.622A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix removed outlier: 3.708A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 221 through 252 removed outlier: 3.799A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 253 through 256 removed outlier: 4.168A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.630A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.837A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.639A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.890A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.993A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 removed outlier: 4.044A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.910A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 481 removed outlier: 3.667A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.536A pdb=" N SER A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.114A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.838A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.895A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.755A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.630A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.988A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'E' and resid 376 through 379 Processing sheet with id=AA5, first strand: chain 'E' and resid 448 through 454 removed outlier: 6.095A pdb=" N TYR E 449 " --> pdb=" O PHE E 497 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N PHE E 497 " --> pdb=" O TYR E 449 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR E 451 " --> pdb=" O TYR E 495 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 271 hydrogen bonds defined for protein. 747 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: 0.80 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1248 1.33 - 1.45: 1531 1.45 - 1.57: 3206 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 6041 Sorted by residual: bond pdb=" CA SER A 331 " pdb=" CB SER A 331 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.55e-02 4.16e+03 1.40e+01 bond pdb=" C THR E 478 " pdb=" N PRO E 479 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.25e-02 6.40e+03 1.14e+01 bond pdb=" N VAL E 483 " pdb=" CA VAL E 483 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.15e-02 7.56e+03 8.70e+00 bond pdb=" N SER A 331 " pdb=" CA SER A 331 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.22e-02 6.72e+03 6.28e+00 bond pdb=" C GLU A 22 " pdb=" O GLU A 22 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.19e-02 7.06e+03 5.92e+00 ... (remaining 6036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 7920 1.79 - 3.59: 235 3.59 - 5.38: 42 5.38 - 7.18: 9 7.18 - 8.97: 3 Bond angle restraints: 8209 Sorted by residual: angle pdb=" N ASN E 481 " pdb=" CA ASN E 481 " pdb=" C ASN E 481 " ideal model delta sigma weight residual 112.97 104.76 8.21 1.06e+00 8.90e-01 6.00e+01 angle pdb=" N GLY E 482 " pdb=" CA GLY E 482 " pdb=" C GLY E 482 " ideal model delta sigma weight residual 115.30 106.84 8.46 1.39e+00 5.18e-01 3.71e+01 angle pdb=" N PRO E 479 " pdb=" CA PRO E 479 " pdb=" C PRO E 479 " ideal model delta sigma weight residual 111.22 118.06 -6.84 1.40e+00 5.10e-01 2.39e+01 angle pdb=" CA CYS E 480 " pdb=" C CYS E 480 " pdb=" N ASN E 481 " ideal model delta sigma weight residual 115.51 120.83 -5.32 1.24e+00 6.50e-01 1.84e+01 angle pdb=" C ASN A 330 " pdb=" CA ASN A 330 " pdb=" CB ASN A 330 " ideal model delta sigma weight residual 111.02 104.86 6.16 1.62e+00 3.81e-01 1.44e+01 ... (remaining 8204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 3210 16.40 - 32.79: 282 32.79 - 49.19: 52 49.19 - 65.58: 16 65.58 - 81.98: 4 Dihedral angle restraints: 3564 sinusoidal: 1426 harmonic: 2138 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual -86.00 -121.93 35.93 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CA TYR A 252 " pdb=" C TYR A 252 " pdb=" N PRO A 253 " pdb=" CA PRO A 253 " ideal model delta harmonic sigma weight residual -180.00 -161.11 -18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA PRO A 389 " pdb=" C PRO A 389 " pdb=" N PHE A 390 " pdb=" CA PHE A 390 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 652 0.053 - 0.105: 187 0.105 - 0.158: 31 0.158 - 0.210: 1 0.210 - 0.263: 2 Chirality restraints: 873 Sorted by residual: chirality pdb=" CA ASN E 481 " pdb=" N ASN E 481 " pdb=" C ASN E 481 " pdb=" CB ASN E 481 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO E 479 " pdb=" N PRO E 479 " pdb=" C PRO E 479 " pdb=" CB PRO E 479 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB ILE A 21 " pdb=" CA ILE A 21 " pdb=" CG1 ILE A 21 " pdb=" CG2 ILE A 21 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 870 not shown) Planarity restraints: 1049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 495 " 0.023 2.00e-02 2.50e+03 1.35e-02 3.67e+00 pdb=" CG TYR E 495 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR E 495 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR E 495 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 495 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 495 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 495 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 495 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 21 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C ILE A 21 " -0.033 2.00e-02 2.50e+03 pdb=" O ILE A 21 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 22 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " -0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 235 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.026 5.00e-02 4.00e+02 ... (remaining 1046 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 37 2.60 - 3.17: 4671 3.17 - 3.75: 8205 3.75 - 4.32: 12466 4.32 - 4.90: 21205 Nonbonded interactions: 46584 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.021 2.230 nonbonded pdb=" OG SER A 19 " pdb=" OE1 GLU A 23 " model vdw 2.175 3.040 nonbonded pdb=" O SER E 438 " pdb=" OG SER E 438 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.284 3.040 nonbonded pdb=" OE2 GLU A 435 " pdb=" NZ LYS A 541 " model vdw 2.289 3.120 ... (remaining 46579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.320 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 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 : 0.008 0.239 6049 Z= 0.325 Angle : 0.881 30.948 8224 Z= 0.488 Chirality : 0.050 0.263 873 Planarity : 0.005 0.046 1046 Dihedral : 13.182 81.978 2183 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.33 % Allowed : 3.98 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.27), residues: 718 helix: -1.42 (0.24), residues: 375 sheet: -2.04 (0.69), residues: 41 loop : -2.83 (0.28), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 393 TYR 0.030 0.002 TYR E 495 PHE 0.014 0.002 PHE A 512 TRP 0.015 0.002 TRP E 353 HIS 0.010 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00687 ( 6041) covalent geometry : angle 0.76689 ( 8209) SS BOND : bond 0.02331 ( 3) SS BOND : angle 15.54428 ( 6) hydrogen bonds : bond 0.18582 ( 271) hydrogen bonds : angle 6.07040 ( 747) metal coordination : bond 0.17157 ( 2) link_NAG-ASN : bond 0.00609 ( 3) link_NAG-ASN : angle 3.52074 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.150 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 67 average time/residue: 0.5441 time to fit residues: 38.3239 Evaluate side-chains 49 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 597 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 374 HIS A 380 GLN E 354 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.079582 restraints weight = 10349.690| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.70 r_work: 0.2918 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.661 6049 Z= 0.307 Angle : 0.508 5.281 8224 Z= 0.268 Chirality : 0.040 0.130 873 Planarity : 0.004 0.031 1046 Dihedral : 5.048 44.946 857 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.66 % Allowed : 9.45 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.29), residues: 718 helix: -0.03 (0.28), residues: 372 sheet: -1.00 (0.66), residues: 49 loop : -2.25 (0.29), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 559 TYR 0.019 0.001 TYR E 495 PHE 0.009 0.001 PHE E 377 TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6041) covalent geometry : angle 0.50370 ( 8209) SS BOND : bond 0.00328 ( 3) SS BOND : angle 0.85094 ( 6) hydrogen bonds : bond 0.05910 ( 271) hydrogen bonds : angle 4.31424 ( 747) metal coordination : bond 0.46748 ( 2) link_NAG-ASN : bond 0.00134 ( 3) link_NAG-ASN : angle 2.07090 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: E 408 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7128 (ptm160) REVERT: E 469 SER cc_start: 0.8228 (m) cc_final: 0.8018 (m) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 0.5032 time to fit residues: 31.3499 Evaluate side-chains 55 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 71 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 57 optimal weight: 0.0770 chunk 23 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS E 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.095923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.080323 restraints weight = 10170.788| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.78 r_work: 0.2939 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6049 Z= 0.103 Angle : 0.464 5.271 8224 Z= 0.241 Chirality : 0.039 0.131 873 Planarity : 0.003 0.032 1046 Dihedral : 4.218 38.771 855 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.83 % Allowed : 10.61 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.31), residues: 718 helix: 0.76 (0.28), residues: 374 sheet: -0.24 (0.83), residues: 37 loop : -1.84 (0.30), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 482 TYR 0.019 0.001 TYR E 495 PHE 0.009 0.001 PHE E 342 TRP 0.008 0.001 TRP E 436 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 6041) covalent geometry : angle 0.45959 ( 8209) SS BOND : bond 0.00037 ( 3) SS BOND : angle 0.81901 ( 6) hydrogen bonds : bond 0.05227 ( 271) hydrogen bonds : angle 3.92655 ( 747) metal coordination : bond 0.00603 ( 2) link_NAG-ASN : bond 0.00185 ( 3) link_NAG-ASN : angle 1.87136 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7496 (mtp) cc_final: 0.7277 (mtp) REVERT: A 70 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8102 (m) REVERT: A 325 GLN cc_start: 0.7770 (tp-100) cc_final: 0.7106 (tm-30) REVERT: E 354 ASN cc_start: 0.7278 (m-40) cc_final: 0.6989 (m-40) REVERT: E 408 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7150 (ptm160) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 0.5079 time to fit residues: 32.1894 Evaluate side-chains 55 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 0.0370 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** 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 = 0.3338 r_free = 0.3338 target = 0.097715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.082182 restraints weight = 10207.409| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.80 r_work: 0.2966 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 6049 Z= 0.092 Angle : 0.440 5.301 8224 Z= 0.227 Chirality : 0.038 0.130 873 Planarity : 0.003 0.031 1046 Dihedral : 3.781 30.398 854 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.16 % Allowed : 12.27 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.31), residues: 718 helix: 1.20 (0.29), residues: 374 sheet: 0.21 (0.87), residues: 37 loop : -1.62 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 482 TYR 0.016 0.001 TYR E 495 PHE 0.007 0.001 PHE A 452 TRP 0.007 0.001 TRP E 436 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 6041) covalent geometry : angle 0.43599 ( 8209) SS BOND : bond 0.00031 ( 3) SS BOND : angle 0.85857 ( 6) hydrogen bonds : bond 0.04541 ( 271) hydrogen bonds : angle 3.77929 ( 747) metal coordination : bond 0.00216 ( 2) link_NAG-ASN : bond 0.00090 ( 3) link_NAG-ASN : angle 1.62621 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8134 (m) REVERT: E 354 ASN cc_start: 0.7328 (m-40) cc_final: 0.7086 (m-40) REVERT: E 408 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7176 (ptm160) outliers start: 7 outliers final: 2 residues processed: 64 average time/residue: 0.5179 time to fit residues: 34.8118 Evaluate side-chains 54 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 408 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 71 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.095104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.079342 restraints weight = 10333.461| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.83 r_work: 0.2911 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6049 Z= 0.112 Angle : 0.464 5.414 8224 Z= 0.239 Chirality : 0.039 0.134 873 Planarity : 0.003 0.031 1046 Dihedral : 3.739 24.767 854 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.33 % Allowed : 12.60 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.32), residues: 718 helix: 1.39 (0.29), residues: 372 sheet: 0.33 (0.87), residues: 37 loop : -1.51 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 482 TYR 0.020 0.001 TYR E 495 PHE 0.008 0.001 PHE A 452 TRP 0.007 0.001 TRP A 477 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6041) covalent geometry : angle 0.46024 ( 8209) SS BOND : bond 0.00087 ( 3) SS BOND : angle 0.75826 ( 6) hydrogen bonds : bond 0.05307 ( 271) hydrogen bonds : angle 3.84108 ( 747) metal coordination : bond 0.00046 ( 2) link_NAG-ASN : bond 0.00051 ( 3) link_NAG-ASN : angle 1.87299 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.8566 (OUTLIER) cc_final: 0.8139 (m) REVERT: A 325 GLN cc_start: 0.7791 (tp40) cc_final: 0.6929 (tm-30) REVERT: A 527 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: E 354 ASN cc_start: 0.7382 (m-40) cc_final: 0.7116 (m-40) outliers start: 8 outliers final: 1 residues processed: 57 average time/residue: 0.5620 time to fit residues: 33.6116 Evaluate side-chains 52 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain E residue 375 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** 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 = 0.3263 r_free = 0.3263 target = 0.092760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.076822 restraints weight = 10169.160| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.85 r_work: 0.2876 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6049 Z= 0.136 Angle : 0.489 5.492 8224 Z= 0.254 Chirality : 0.040 0.138 873 Planarity : 0.003 0.030 1046 Dihedral : 3.854 20.370 854 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.49 % Allowed : 12.60 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.32), residues: 718 helix: 1.39 (0.29), residues: 373 sheet: 0.14 (0.76), residues: 47 loop : -1.47 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 482 TYR 0.022 0.001 TYR E 495 PHE 0.008 0.001 PHE A 523 TRP 0.008 0.001 TRP A 477 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6041) covalent geometry : angle 0.48379 ( 8209) SS BOND : bond 0.00293 ( 3) SS BOND : angle 0.84321 ( 6) hydrogen bonds : bond 0.06098 ( 271) hydrogen bonds : angle 3.98016 ( 747) metal coordination : bond 0.00066 ( 2) link_NAG-ASN : bond 0.00086 ( 3) link_NAG-ASN : angle 2.10371 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8148 (m) REVERT: A 325 GLN cc_start: 0.7851 (tp40) cc_final: 0.7022 (tm-30) REVERT: A 527 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7161 (tp30) REVERT: E 460 LYS cc_start: 0.9265 (mttt) cc_final: 0.8973 (mttm) outliers start: 9 outliers final: 6 residues processed: 62 average time/residue: 0.5761 time to fit residues: 37.4246 Evaluate side-chains 59 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.094933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.079197 restraints weight = 10143.864| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.81 r_work: 0.2918 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6049 Z= 0.105 Angle : 0.463 5.415 8224 Z= 0.237 Chirality : 0.039 0.131 873 Planarity : 0.003 0.030 1046 Dihedral : 3.682 21.874 854 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.66 % Allowed : 13.27 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.32), residues: 718 helix: 1.54 (0.29), residues: 373 sheet: 0.69 (0.91), residues: 37 loop : -1.36 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 482 TYR 0.017 0.001 TYR E 495 PHE 0.007 0.001 PHE A 327 TRP 0.007 0.001 TRP A 477 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 6041) covalent geometry : angle 0.45871 ( 8209) SS BOND : bond 0.00121 ( 3) SS BOND : angle 0.71346 ( 6) hydrogen bonds : bond 0.05132 ( 271) hydrogen bonds : angle 3.86077 ( 747) metal coordination : bond 0.00050 ( 2) link_NAG-ASN : bond 0.00076 ( 3) link_NAG-ASN : angle 1.90445 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.8170 (m) REVERT: A 325 GLN cc_start: 0.7813 (tp40) cc_final: 0.7002 (tm-30) REVERT: A 527 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7120 (tp30) REVERT: E 460 LYS cc_start: 0.9290 (mttt) cc_final: 0.9001 (mttm) outliers start: 10 outliers final: 6 residues processed: 62 average time/residue: 0.5680 time to fit residues: 36.9324 Evaluate side-chains 58 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 478 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 0.0270 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 0.0270 chunk 8 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.1698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** 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 = 0.3287 r_free = 0.3287 target = 0.094245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.078474 restraints weight = 10172.140| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.82 r_work: 0.2911 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6049 Z= 0.115 Angle : 0.479 6.189 8224 Z= 0.245 Chirality : 0.040 0.133 873 Planarity : 0.003 0.030 1046 Dihedral : 3.667 20.503 854 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.99 % Allowed : 13.93 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.32), residues: 718 helix: 1.58 (0.29), residues: 373 sheet: 0.72 (0.91), residues: 37 loop : -1.32 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 482 TYR 0.019 0.001 TYR E 495 PHE 0.008 0.001 PHE A 452 TRP 0.007 0.001 TRP E 436 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6041) covalent geometry : angle 0.47440 ( 8209) SS BOND : bond 0.00120 ( 3) SS BOND : angle 0.70553 ( 6) hydrogen bonds : bond 0.05421 ( 271) hydrogen bonds : angle 3.88085 ( 747) metal coordination : bond 0.00042 ( 2) link_NAG-ASN : bond 0.00067 ( 3) link_NAG-ASN : angle 1.98565 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8171 (m) REVERT: A 325 GLN cc_start: 0.7821 (tp40) cc_final: 0.6989 (tm-30) REVERT: A 527 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7104 (tp30) REVERT: E 460 LYS cc_start: 0.9289 (mttt) cc_final: 0.8999 (mttm) outliers start: 12 outliers final: 7 residues processed: 61 average time/residue: 0.5840 time to fit residues: 37.3405 Evaluate side-chains 62 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 478 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 68 optimal weight: 1.9990 chunk 31 optimal weight: 0.0030 chunk 48 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 0.0000 chunk 24 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 65 optimal weight: 0.0770 chunk 66 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 overall best weight: 0.2952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.099516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.084048 restraints weight = 10217.016| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.80 r_work: 0.3005 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6049 Z= 0.087 Angle : 0.442 5.828 8224 Z= 0.222 Chirality : 0.038 0.127 873 Planarity : 0.003 0.030 1046 Dihedral : 3.391 21.233 854 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.16 % Allowed : 14.76 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.32), residues: 718 helix: 1.72 (0.29), residues: 373 sheet: 0.90 (0.93), residues: 37 loop : -1.17 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 115 TYR 0.015 0.001 TYR A 183 PHE 0.006 0.001 PHE A 28 TRP 0.008 0.001 TRP E 436 HIS 0.002 0.000 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00168 ( 6041) covalent geometry : angle 0.43941 ( 8209) SS BOND : bond 0.00101 ( 3) SS BOND : angle 0.57773 ( 6) hydrogen bonds : bond 0.03961 ( 271) hydrogen bonds : angle 3.73881 ( 747) metal coordination : bond 0.00098 ( 2) link_NAG-ASN : bond 0.00097 ( 3) link_NAG-ASN : angle 1.53985 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8188 (m) REVERT: E 460 LYS cc_start: 0.9306 (mttt) cc_final: 0.9006 (mttm) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.5570 time to fit residues: 34.5549 Evaluate side-chains 60 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 325 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.082429 restraints weight = 10277.914| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.85 r_work: 0.2977 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6049 Z= 0.092 Angle : 0.448 5.711 8224 Z= 0.226 Chirality : 0.038 0.127 873 Planarity : 0.003 0.030 1046 Dihedral : 3.325 19.225 854 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.16 % Allowed : 14.59 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.32), residues: 718 helix: 1.80 (0.28), residues: 373 sheet: 0.98 (0.93), residues: 37 loop : -1.11 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 482 TYR 0.016 0.001 TYR A 183 PHE 0.007 0.001 PHE A 452 TRP 0.007 0.001 TRP E 436 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 6041) covalent geometry : angle 0.44479 ( 8209) SS BOND : bond 0.00090 ( 3) SS BOND : angle 0.55240 ( 6) hydrogen bonds : bond 0.04325 ( 271) hydrogen bonds : angle 3.71395 ( 747) metal coordination : bond 0.00021 ( 2) link_NAG-ASN : bond 0.00070 ( 3) link_NAG-ASN : angle 1.64986 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.8189 (m) REVERT: A 325 GLN cc_start: 0.7780 (tp40) cc_final: 0.7013 (tm-30) REVERT: E 460 LYS cc_start: 0.9313 (mttt) cc_final: 0.9014 (mttm) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.5378 time to fit residues: 33.4238 Evaluate side-chains 61 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 62 optimal weight: 5.9990 chunk 25 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.079423 restraints weight = 10207.430| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.84 r_work: 0.2923 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6049 Z= 0.113 Angle : 0.477 5.809 8224 Z= 0.242 Chirality : 0.039 0.133 873 Planarity : 0.003 0.030 1046 Dihedral : 3.468 17.406 854 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.16 % Allowed : 14.76 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.32), residues: 718 helix: 1.79 (0.28), residues: 373 sheet: 0.99 (0.93), residues: 37 loop : -1.11 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 482 TYR 0.019 0.001 TYR E 495 PHE 0.008 0.001 PHE A 452 TRP 0.007 0.001 TRP A 477 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6041) covalent geometry : angle 0.47343 ( 8209) SS BOND : bond 0.00099 ( 3) SS BOND : angle 0.63957 ( 6) hydrogen bonds : bond 0.05199 ( 271) hydrogen bonds : angle 3.81003 ( 747) metal coordination : bond 0.00047 ( 2) link_NAG-ASN : bond 0.00065 ( 3) link_NAG-ASN : angle 1.84033 ( 9) =============================================================================== Job complete usr+sys time: 1644.27 seconds wall clock time: 28 minutes 47.80 seconds (1727.80 seconds total)