Starting phenix.real_space_refine on Fri Dec 27 20:30:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xza_38791/12_2024/8xza_38791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xza_38791/12_2024/8xza_38791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xza_38791/12_2024/8xza_38791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xza_38791/12_2024/8xza_38791.map" model { file = "/net/cci-nas-00/data/ceres_data/8xza_38791/12_2024/8xza_38791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xza_38791/12_2024/8xza_38791.cif" } resolution = 4.07 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= -0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 38 5.16 5 Cl 1 4.86 5 C 4202 2.51 5 N 1083 2.21 5 O 1240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6565 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 13, 'TRANS': 180} Chain: "A" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4906 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 571} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 72 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.66, per 1000 atoms: 0.71 Number of scatterers: 6565 At special positions: 0 Unit cell: (79, 100, 109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 38 16.00 O 1240 8.00 N 1083 7.00 C 4202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 524 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 487 " distance=2.02 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 360 " distance=2.02 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 53 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 298 " " NAG A 905 " - " ASN A 431 " " NAG A 906 " - " ASN A 545 " " NAG B1302 " - " ASN B 343 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 912.1 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 56.2% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.770A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.590A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.870A pdb=" N GLU A 87 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.509A pdb=" N HIS A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 156 through 193 removed outlier: 3.519A pdb=" N ARG A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 219 through 251 Proline residue: A 234 - end of helix Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 292 through 300 Processing helix chain 'A' and resid 302 through 316 Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.895A pdb=" N TRP A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 384 removed outlier: 3.630A pdb=" N PHE A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.667A pdb=" N ALA A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 removed outlier: 3.665A pdb=" N LEU A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 444 Processing helix chain 'A' and resid 447 through 465 removed outlier: 4.615A pdb=" N PHE A 451 " --> pdb=" O GLY A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 483 Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 511 through 532 removed outlier: 3.602A pdb=" N TYR A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 546 through 558 removed outlier: 3.872A pdb=" N MET A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 580 through 587 removed outlier: 3.795A pdb=" N PHE A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 598 Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing sheet with id=AA1, first strand: chain 'B' and resid 355 through 358 Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.534A pdb=" N LEU A 141 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 261 through 262 removed outlier: 6.710A pdb=" N LEU A 261 " --> pdb=" O VAL A 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 299 hydrogen bonds defined for protein. 864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1198 1.32 - 1.45: 1924 1.45 - 1.57: 3570 1.57 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 6752 Sorted by residual: bond pdb=" CA SER B 438 " pdb=" C SER B 438 " ideal model delta sigma weight residual 1.522 1.419 0.103 1.08e-02 8.57e+03 9.10e+01 bond pdb=" CA ALA B 352 " pdb=" C ALA B 352 " ideal model delta sigma weight residual 1.530 1.476 0.055 1.08e-02 8.57e+03 2.58e+01 bond pdb=" CA ASN B 439 " pdb=" C ASN B 439 " ideal model delta sigma weight residual 1.522 1.475 0.047 9.30e-03 1.16e+04 2.52e+01 bond pdb=" CA ARG B 466 " pdb=" C ARG B 466 " ideal model delta sigma weight residual 1.524 1.464 0.060 1.25e-02 6.40e+03 2.31e+01 bond pdb=" CA SER B 443 " pdb=" C SER B 443 " ideal model delta sigma weight residual 1.528 1.466 0.061 1.37e-02 5.33e+03 2.00e+01 ... (remaining 6747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 8906 3.03 - 6.07: 220 6.07 - 9.10: 31 9.10 - 12.13: 3 12.13 - 15.17: 4 Bond angle restraints: 9164 Sorted by residual: angle pdb=" N GLY B 447 " pdb=" CA GLY B 447 " pdb=" C GLY B 447 " ideal model delta sigma weight residual 111.95 125.46 -13.51 9.50e-01 1.11e+00 2.02e+02 angle pdb=" N GLY B 482 " pdb=" CA GLY B 482 " pdb=" C GLY B 482 " ideal model delta sigma weight residual 110.60 123.34 -12.74 1.46e+00 4.69e-01 7.62e+01 angle pdb=" N LYS B 481 " pdb=" CA LYS B 481 " pdb=" C LYS B 481 " ideal model delta sigma weight residual 111.11 100.80 10.31 1.20e+00 6.94e-01 7.38e+01 angle pdb=" N ALA B 352 " pdb=" CA ALA B 352 " pdb=" C ALA B 352 " ideal model delta sigma weight residual 107.32 93.57 13.75 1.65e+00 3.67e-01 6.94e+01 angle pdb=" N PHE B 400 " pdb=" CA PHE B 400 " pdb=" C PHE B 400 " ideal model delta sigma weight residual 109.63 121.74 -12.11 1.49e+00 4.50e-01 6.61e+01 ... (remaining 9159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 3803 23.80 - 47.59: 221 47.59 - 71.38: 28 71.38 - 95.18: 9 95.18 - 118.97: 14 Dihedral angle restraints: 4075 sinusoidal: 1746 harmonic: 2329 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 487 " pdb=" CB CYS B 487 " ideal model delta sinusoidal sigma weight residual -86.00 -158.70 72.70 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 44.40 48.60 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" CA MET A 62 " pdb=" C MET A 62 " pdb=" N ASN A 63 " pdb=" CA ASN A 63 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 4072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 822 0.075 - 0.150: 124 0.150 - 0.225: 16 0.225 - 0.300: 3 0.300 - 0.375: 3 Chirality restraints: 968 Sorted by residual: chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C1 NAG A 904 " pdb=" ND2 ASN A 298 " pdb=" C2 NAG A 904 " pdb=" O5 NAG A 904 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA TRP B 353 " pdb=" N TRP B 353 " pdb=" C TRP B 353 " pdb=" CB TRP B 353 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 965 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " 0.297 2.00e-02 2.50e+03 2.53e-01 8.02e+02 pdb=" C7 NAG B1301 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " -0.018 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " -0.425 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " 0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 350 " -0.043 2.00e-02 2.50e+03 8.82e-02 7.78e+01 pdb=" C VAL B 350 " 0.152 2.00e-02 2.50e+03 pdb=" O VAL B 350 " -0.059 2.00e-02 2.50e+03 pdb=" N TYR B 351 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 345 " 0.031 2.00e-02 2.50e+03 6.23e-02 3.88e+01 pdb=" C THR B 345 " -0.108 2.00e-02 2.50e+03 pdb=" O THR B 345 " 0.040 2.00e-02 2.50e+03 pdb=" N ARG B 346 " 0.037 2.00e-02 2.50e+03 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.95: 4 1.95 - 2.69: 278 2.69 - 3.42: 10143 3.42 - 4.16: 16088 4.16 - 4.90: 27724 Nonbonded interactions: 54237 Sorted by model distance: nonbonded pdb=" CD2 TYR B 351 " pdb=" O TRP B 452 " model vdw 1.212 3.340 nonbonded pdb=" CZ3 TRP B 353 " pdb=" CB ARG B 355 " model vdw 1.659 3.740 nonbonded pdb=" CE2 TYR B 351 " pdb=" O TRP B 452 " model vdw 1.746 3.340 nonbonded pdb=" OH TYR A 242 " pdb=" O LEU A 594 " model vdw 1.927 3.040 nonbonded pdb=" OG SER B 349 " pdb=" CE2 TYR B 351 " model vdw 1.982 3.340 ... (remaining 54232 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 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: 2.300 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.610 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 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 : 0.007 0.103 6752 Z= 0.440 Angle : 1.099 15.168 9164 Z= 0.641 Chirality : 0.058 0.375 968 Planarity : 0.010 0.253 1168 Dihedral : 16.313 118.973 2566 Min Nonbonded Distance : 1.212 Molprobity Statistics. All-atom Clashscore : 30.95 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.02 % Favored : 91.09 % Rotamer: Outliers : 0.14 % Allowed : 2.02 % Favored : 97.84 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.70 % 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: -1.65 (0.28), residues: 786 helix: -0.42 (0.25), residues: 393 sheet: -0.89 (0.99), residues: 31 loop : -1.85 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 164 HIS 0.008 0.001 HIS A 264 PHE 0.030 0.003 PHE A 437 TYR 0.055 0.003 TYR A 453 ARG 0.004 0.001 ARG A 558 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.7243 (mp0) cc_final: 0.6369 (tp30) REVERT: B 514 PHE cc_start: 0.6054 (m-80) cc_final: 0.5758 (m-10) REVERT: A 100 LEU cc_start: 0.8461 (mt) cc_final: 0.8260 (mt) REVERT: A 248 MET cc_start: 0.7022 (ptm) cc_final: 0.6781 (ppp) REVERT: A 455 LEU cc_start: 0.9450 (mt) cc_final: 0.9067 (mt) REVERT: A 458 TRP cc_start: 0.7185 (m100) cc_final: 0.6846 (m100) REVERT: A 557 LEU cc_start: 0.8950 (mt) cc_final: 0.8523 (mt) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.2070 time to fit residues: 40.6162 Evaluate side-chains 98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 0.0770 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 474 GLN B 492 GLN A 33 ASN A 42 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6752 Z= 0.252 Angle : 0.765 7.915 9164 Z= 0.390 Chirality : 0.050 0.385 968 Planarity : 0.005 0.044 1168 Dihedral : 10.262 108.064 1016 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % Rotamer: Outliers : 0.14 % Allowed : 6.64 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.30 (0.29), residues: 786 helix: -0.17 (0.25), residues: 397 sheet: -0.35 (0.93), residues: 31 loop : -1.68 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 353 HIS 0.006 0.001 HIS A 264 PHE 0.017 0.002 PHE B 347 TYR 0.047 0.003 TYR A 453 ARG 0.004 0.001 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 LYS cc_start: 0.7832 (mtmt) cc_final: 0.7366 (mtpt) REVERT: B 499 THR cc_start: 0.8524 (p) cc_final: 0.8274 (p) REVERT: A 79 MET cc_start: 0.8672 (tpp) cc_final: 0.8192 (tpp) REVERT: A 100 LEU cc_start: 0.8683 (mt) cc_final: 0.8434 (mt) REVERT: A 123 MET cc_start: 0.8242 (mtm) cc_final: 0.7998 (mtm) REVERT: A 248 MET cc_start: 0.7163 (ptm) cc_final: 0.6881 (ppp) REVERT: A 455 LEU cc_start: 0.9563 (mt) cc_final: 0.9145 (mt) REVERT: A 458 TRP cc_start: 0.7235 (m100) cc_final: 0.6784 (m100) REVERT: A 479 MET cc_start: 0.8966 (ppp) cc_final: 0.8697 (ppp) REVERT: A 516 THR cc_start: 0.9005 (p) cc_final: 0.8531 (p) REVERT: A 557 LEU cc_start: 0.8945 (mt) cc_final: 0.8558 (mt) REVERT: A 567 LEU cc_start: 0.9001 (tp) cc_final: 0.8793 (tp) outliers start: 1 outliers final: 1 residues processed: 140 average time/residue: 0.1781 time to fit residues: 33.5996 Evaluate side-chains 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN A 33 ASN A 42 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6752 Z= 0.272 Angle : 0.735 9.433 9164 Z= 0.377 Chirality : 0.049 0.330 968 Planarity : 0.005 0.045 1168 Dihedral : 9.133 99.262 1016 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.53 % Rotamer: Outliers : 0.14 % Allowed : 4.47 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.18 (0.29), residues: 786 helix: -0.14 (0.25), residues: 401 sheet: -0.01 (0.94), residues: 31 loop : -1.57 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 353 HIS 0.006 0.001 HIS A 264 PHE 0.019 0.002 PHE A 451 TYR 0.063 0.002 TYR A 453 ARG 0.005 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 LYS cc_start: 0.7747 (mtmt) cc_final: 0.7345 (mtpt) REVERT: B 499 THR cc_start: 0.8551 (p) cc_final: 0.8301 (p) REVERT: A 79 MET cc_start: 0.8709 (tpp) cc_final: 0.8218 (tpp) REVERT: A 100 LEU cc_start: 0.8643 (mt) cc_final: 0.8426 (mt) REVERT: A 248 MET cc_start: 0.7359 (ptm) cc_final: 0.7110 (ppp) REVERT: A 326 PHE cc_start: 0.6622 (m-80) cc_final: 0.5908 (m-80) REVERT: A 440 LYS cc_start: 0.8111 (tmtt) cc_final: 0.7906 (ttpt) REVERT: A 458 TRP cc_start: 0.7305 (m100) cc_final: 0.6717 (m100) REVERT: A 479 MET cc_start: 0.8998 (ppp) cc_final: 0.8739 (ppp) REVERT: A 515 TYR cc_start: 0.7777 (t80) cc_final: 0.7472 (t80) REVERT: A 516 THR cc_start: 0.8994 (p) cc_final: 0.8409 (p) REVERT: A 567 LEU cc_start: 0.9025 (tp) cc_final: 0.8788 (tp) REVERT: A 588 GLU cc_start: 0.8532 (mt-10) cc_final: 0.7989 (mm-30) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.1894 time to fit residues: 32.9137 Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6752 Z= 0.256 Angle : 0.726 8.607 9164 Z= 0.370 Chirality : 0.049 0.343 968 Planarity : 0.005 0.055 1168 Dihedral : 8.726 92.862 1016 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.14 (0.29), residues: 786 helix: -0.18 (0.25), residues: 406 sheet: -0.35 (0.94), residues: 29 loop : -1.42 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 353 HIS 0.006 0.001 HIS A 525 PHE 0.020 0.002 PHE A 437 TYR 0.049 0.002 TYR A 453 ARG 0.008 0.001 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7527 (mtpt) REVERT: B 499 THR cc_start: 0.8437 (p) cc_final: 0.8136 (p) REVERT: A 100 LEU cc_start: 0.8670 (mt) cc_final: 0.8418 (mt) REVERT: A 164 TRP cc_start: 0.7113 (m-90) cc_final: 0.6867 (m-90) REVERT: A 248 MET cc_start: 0.7407 (ptm) cc_final: 0.7174 (ppp) REVERT: A 302 ASP cc_start: 0.8085 (t70) cc_final: 0.7821 (t70) REVERT: A 326 PHE cc_start: 0.6652 (m-80) cc_final: 0.6051 (m-80) REVERT: A 453 TYR cc_start: 0.6137 (m-80) cc_final: 0.5663 (m-80) REVERT: A 515 TYR cc_start: 0.7757 (t80) cc_final: 0.7435 (t80) REVERT: A 522 PHE cc_start: 0.8859 (m-10) cc_final: 0.8595 (m-10) REVERT: A 567 LEU cc_start: 0.9070 (tp) cc_final: 0.8837 (tp) REVERT: A 588 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8040 (mm-30) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1679 time to fit residues: 29.2039 Evaluate side-chains 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.0370 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 GLN A 525 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6752 Z= 0.210 Angle : 0.724 9.180 9164 Z= 0.366 Chirality : 0.050 0.493 968 Planarity : 0.004 0.047 1168 Dihedral : 8.175 85.900 1016 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % Rotamer: Outliers : 0.14 % Allowed : 3.32 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.95 (0.29), residues: 786 helix: -0.03 (0.26), residues: 400 sheet: -0.29 (0.94), residues: 29 loop : -1.30 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 353 HIS 0.005 0.001 HIS A 525 PHE 0.018 0.002 PHE A 437 TYR 0.040 0.002 TYR A 453 ARG 0.004 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 424 LYS cc_start: 0.6822 (ttmt) cc_final: 0.6565 (tptt) REVERT: B 499 THR cc_start: 0.8438 (p) cc_final: 0.8152 (p) REVERT: A 164 TRP cc_start: 0.7154 (m-90) cc_final: 0.6901 (m-90) REVERT: A 248 MET cc_start: 0.7378 (ptm) cc_final: 0.7129 (ppp) REVERT: A 254 TYR cc_start: 0.7164 (m-80) cc_final: 0.6959 (m-80) REVERT: A 302 ASP cc_start: 0.8179 (t70) cc_final: 0.7888 (t70) REVERT: A 326 PHE cc_start: 0.6601 (m-80) cc_final: 0.6208 (m-80) REVERT: A 446 VAL cc_start: 0.8776 (m) cc_final: 0.8452 (p) REVERT: A 453 TYR cc_start: 0.5896 (m-80) cc_final: 0.4788 (m-80) REVERT: A 515 TYR cc_start: 0.7792 (t80) cc_final: 0.7485 (t80) REVERT: A 557 LEU cc_start: 0.8963 (mm) cc_final: 0.8658 (mm) REVERT: A 588 GLU cc_start: 0.8586 (mt-10) cc_final: 0.7999 (mm-30) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1784 time to fit residues: 33.6171 Evaluate side-chains 100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6752 Z= 0.225 Angle : 0.718 9.698 9164 Z= 0.364 Chirality : 0.049 0.401 968 Planarity : 0.004 0.048 1168 Dihedral : 7.674 72.830 1016 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.53 % Rotamer: Outliers : 0.14 % Allowed : 2.60 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.88 (0.29), residues: 786 helix: -0.01 (0.25), residues: 401 sheet: -0.16 (0.95), residues: 29 loop : -1.22 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 353 HIS 0.006 0.001 HIS A 525 PHE 0.018 0.002 PHE A 28 TYR 0.045 0.002 TYR A 50 ARG 0.004 0.001 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 424 LYS cc_start: 0.6983 (ttmt) cc_final: 0.6596 (tptt) REVERT: B 499 THR cc_start: 0.8403 (p) cc_final: 0.8123 (p) REVERT: A 151 MET cc_start: 0.6798 (tpt) cc_final: 0.5945 (tpp) REVERT: A 164 TRP cc_start: 0.7318 (m-90) cc_final: 0.7105 (m-90) REVERT: A 248 MET cc_start: 0.7512 (ptm) cc_final: 0.7287 (ppp) REVERT: A 274 TRP cc_start: 0.8311 (m-10) cc_final: 0.8019 (m-10) REVERT: A 302 ASP cc_start: 0.8249 (t70) cc_final: 0.8022 (t70) REVERT: A 326 PHE cc_start: 0.6082 (m-80) cc_final: 0.5851 (m-80) REVERT: A 446 VAL cc_start: 0.8776 (m) cc_final: 0.8495 (p) REVERT: A 453 TYR cc_start: 0.5806 (m-80) cc_final: 0.4992 (m-80) REVERT: A 455 LEU cc_start: 0.9370 (mt) cc_final: 0.8986 (mt) REVERT: A 557 LEU cc_start: 0.9062 (mm) cc_final: 0.8761 (mm) REVERT: A 588 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8072 (mm-30) outliers start: 1 outliers final: 1 residues processed: 136 average time/residue: 0.1671 time to fit residues: 31.0775 Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.0010 chunk 44 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6752 Z= 0.213 Angle : 0.730 10.935 9164 Z= 0.367 Chirality : 0.050 0.455 968 Planarity : 0.004 0.047 1168 Dihedral : 7.197 54.843 1016 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.83 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.94 (0.29), residues: 786 helix: -0.07 (0.25), residues: 409 sheet: -0.20 (0.96), residues: 29 loop : -1.26 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 353 HIS 0.006 0.001 HIS A 525 PHE 0.023 0.002 PHE A 229 TYR 0.051 0.002 TYR A 50 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 THR cc_start: 0.8367 (p) cc_final: 0.8068 (p) REVERT: A 151 MET cc_start: 0.6781 (tpt) cc_final: 0.5979 (tpp) REVERT: A 164 TRP cc_start: 0.7329 (m-90) cc_final: 0.7120 (m-90) REVERT: A 248 MET cc_start: 0.7522 (ptm) cc_final: 0.7284 (ppp) REVERT: A 274 TRP cc_start: 0.8292 (m-10) cc_final: 0.8029 (m-10) REVERT: A 302 ASP cc_start: 0.8288 (t70) cc_final: 0.8056 (t70) REVERT: A 326 PHE cc_start: 0.6559 (m-80) cc_final: 0.5782 (m-80) REVERT: A 446 VAL cc_start: 0.8847 (m) cc_final: 0.8589 (p) REVERT: A 453 TYR cc_start: 0.5158 (m-80) cc_final: 0.4542 (m-80) REVERT: A 557 LEU cc_start: 0.8845 (mm) cc_final: 0.8617 (mm) REVERT: A 588 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8106 (mm-30) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1840 time to fit residues: 32.8338 Evaluate side-chains 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6752 Z= 0.206 Angle : 0.733 9.833 9164 Z= 0.373 Chirality : 0.051 0.415 968 Planarity : 0.004 0.046 1168 Dihedral : 6.749 56.151 1016 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.29), residues: 786 helix: 0.02 (0.25), residues: 403 sheet: 0.03 (1.00), residues: 29 loop : -1.18 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 353 HIS 0.005 0.001 HIS A 525 PHE 0.025 0.002 PHE A 229 TYR 0.040 0.002 TYR A 453 ARG 0.005 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 THR cc_start: 0.8453 (p) cc_final: 0.8154 (p) REVERT: A 63 ASN cc_start: 0.8644 (m-40) cc_final: 0.8396 (m-40) REVERT: A 151 MET cc_start: 0.7169 (tpt) cc_final: 0.6254 (tpp) REVERT: A 302 ASP cc_start: 0.8307 (t70) cc_final: 0.8057 (t70) REVERT: A 446 VAL cc_start: 0.8839 (m) cc_final: 0.8636 (p) REVERT: A 453 TYR cc_start: 0.5193 (m-80) cc_final: 0.4379 (m-80) REVERT: A 503 PHE cc_start: 0.8874 (t80) cc_final: 0.8672 (t80) REVERT: A 557 LEU cc_start: 0.8963 (mm) cc_final: 0.8627 (mm) REVERT: A 588 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8135 (mm-30) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1925 time to fit residues: 36.0417 Evaluate side-chains 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6752 Z= 0.216 Angle : 0.727 8.733 9164 Z= 0.370 Chirality : 0.050 0.400 968 Planarity : 0.004 0.048 1168 Dihedral : 6.457 56.434 1016 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.01 (0.29), residues: 786 helix: -0.14 (0.25), residues: 410 sheet: -0.17 (1.01), residues: 30 loop : -1.30 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 353 HIS 0.005 0.001 HIS A 525 PHE 0.028 0.002 PHE A 229 TYR 0.065 0.002 TYR A 50 ARG 0.007 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 THR cc_start: 0.8362 (p) cc_final: 0.8097 (p) REVERT: A 64 GLU cc_start: 0.8970 (mp0) cc_final: 0.8641 (mp0) REVERT: A 302 ASP cc_start: 0.8341 (t70) cc_final: 0.8094 (t70) REVERT: A 322 MET cc_start: 0.6065 (mmm) cc_final: 0.5806 (tpt) REVERT: A 453 TYR cc_start: 0.4841 (m-80) cc_final: 0.4343 (m-80) REVERT: A 557 LEU cc_start: 0.8973 (mm) cc_final: 0.8744 (mm) REVERT: A 588 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8146 (mm-30) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1940 time to fit residues: 36.4302 Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6752 Z= 0.234 Angle : 0.735 9.072 9164 Z= 0.373 Chirality : 0.051 0.405 968 Planarity : 0.004 0.049 1168 Dihedral : 6.437 56.479 1016 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.96 (0.29), residues: 786 helix: -0.11 (0.25), residues: 402 sheet: -0.38 (1.01), residues: 30 loop : -1.21 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 353 HIS 0.006 0.001 HIS A 525 PHE 0.032 0.002 PHE A 229 TYR 0.053 0.002 TYR A 50 ARG 0.006 0.001 ARG A 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 THR cc_start: 0.8361 (p) cc_final: 0.8077 (p) REVERT: A 64 GLU cc_start: 0.8909 (mp0) cc_final: 0.8566 (mp0) REVERT: A 151 MET cc_start: 0.6843 (tpt) cc_final: 0.5923 (tpp) REVERT: A 302 ASP cc_start: 0.8363 (t70) cc_final: 0.8091 (t70) REVERT: A 357 ILE cc_start: 0.8749 (mp) cc_final: 0.8487 (mp) REVERT: A 453 TYR cc_start: 0.4862 (m-80) cc_final: 0.4542 (m-80) REVERT: A 557 LEU cc_start: 0.8961 (mm) cc_final: 0.8708 (mm) REVERT: A 588 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8186 (mm-30) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.1509 time to fit residues: 27.7452 Evaluate side-chains 98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.114612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.091142 restraints weight = 20041.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.094336 restraints weight = 10962.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.096459 restraints weight = 6999.357| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 6752 Z= 0.333 Angle : 0.813 9.608 9164 Z= 0.415 Chirality : 0.053 0.368 968 Planarity : 0.005 0.050 1168 Dihedral : 6.922 54.869 1016 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.11 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.13 (0.29), residues: 786 helix: -0.24 (0.25), residues: 406 sheet: -0.82 (0.88), residues: 40 loop : -1.27 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 348 HIS 0.006 0.001 HIS A 525 PHE 0.041 0.003 PHE A 229 TYR 0.048 0.003 TYR A 453 ARG 0.006 0.001 ARG A 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1754.84 seconds wall clock time: 33 minutes 6.74 seconds (1986.74 seconds total)