Starting phenix.real_space_refine on Thu Jul 2 04:25:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xza_38791/07_2026/8xza_38791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xza_38791/07_2026/8xza_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xza_38791/07_2026/8xza_38791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xza_38791/07_2026/8xza_38791.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xza_38791/07_2026/8xza_38791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xza_38791/07_2026/8xza_38791.map" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 71 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.28, per 1000 atoms: 0.19 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: 0.53 Conformation dependent library (CDL) restraints added in 330.8 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: 0.16 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: 0.77 Time building geometry restraints manager: 0.72 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: 3.430 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 6.570 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 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 6763 Z= 0.430 Angle : 1.111 15.168 9192 Z= 0.643 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 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: -1.65 (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 ARG 0.004 0.001 ARG A 558 TYR 0.055 0.003 TYR A 453 PHE 0.030 0.003 PHE A 437 TRP 0.029 0.003 TRP A 164 HIS 0.008 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.43 ( 6752) covalent geometry : angle 1.09875 / 0.64 ( 9164) SS BOND : bond 0.00548 / 0.33 ( 5) SS BOND : angle 1.79302 / 0.91 ( 10) hydrogen bonds : bond 0.14353 / 8.91 ( 299) hydrogen bonds : angle 6.79056 / 4.91 ( 864) link_NAG-ASN : bond 0.00904 / 0.54 ( 6) link_NAG-ASN : angle 3.65526 / 3.00 ( 18) *********************** 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 : 0.168 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: 0.6053 (m-80) cc_final: 0.5764 (m-10) REVERT: A 248 MET cc_start: 0.7022 (ptm) cc_final: 0.6782 (ppp) REVERT: A 455 LEU cc_start: 0.9450 (mt) cc_final: 0.9070 (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: 0.8526 (mt) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.0647 time to fit residues: 13.0572 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 : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.0170 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0050 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.127931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.104399 restraints weight = 21316.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.107684 restraints weight = 11739.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.109862 restraints weight = 7569.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.111201 restraints weight = 5499.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.112282 restraints weight = 4430.633| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6763 Z= 0.162 Angle : 0.763 9.189 9192 Z= 0.385 Chirality : 0.050 0.394 968 Planarity : 0.005 0.044 1168 Dihedral : 10.229 108.508 1016 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 0.14 % Allowed : 6.06 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.32 (0.29), residues: 786 helix: -0.30 (0.25), residues: 408 sheet: -0.05 (0.94), residues: 30 loop : -1.60 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 466 TYR 0.044 0.002 TYR A 453 PHE 0.016 0.002 PHE A 451 TRP 0.046 0.002 TRP B 353 HIS 0.006 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 6752) covalent geometry : angle 0.75176 / 0.38 ( 9164) SS BOND : bond 0.00123 / 0.06 ( 5) SS BOND : angle 1.09734 / 0.54 ( 10) hydrogen bonds : bond 0.04668 / 3.11 ( 299) hydrogen bonds : angle 5.38975 / 3.78 ( 864) link_NAG-ASN : bond 0.00681 / 0.38 ( 6) link_NAG-ASN : angle 2.95733 / 2.55 ( 18) *********************** 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 : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 LYS cc_start: 0.7771 (mtmt) cc_final: 0.7283 (mtpt) REVERT: B 499 THR cc_start: 0.8592 (p) cc_final: 0.8328 (p) REVERT: A 79 MET cc_start: 0.8787 (tpp) cc_final: 0.8273 (tpp) REVERT: A 100 LEU cc_start: 0.8650 (mt) cc_final: 0.8394 (mt) REVERT: A 248 MET cc_start: 0.7155 (ptm) cc_final: 0.6865 (ppp) REVERT: A 453 TYR cc_start: 0.6499 (m-80) cc_final: 0.6234 (m-80) REVERT: A 455 LEU cc_start: 0.9560 (mt) cc_final: 0.9120 (mt) REVERT: A 458 TRP cc_start: 0.7260 (m100) cc_final: 0.6812 (m100) REVERT: A 479 MET cc_start: 0.8944 (ppp) cc_final: 0.8688 (ppp) REVERT: A 516 THR cc_start: 0.8915 (p) cc_final: 0.8409 (p) REVERT: A 557 LEU cc_start: 0.8970 (mt) cc_final: 0.8608 (mt) REVERT: A 588 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7720 (mm-30) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.0633 time to fit residues: 12.1614 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 : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN A 33 ASN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS A 299 GLN A 525 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.125362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.101567 restraints weight = 21271.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.104794 restraints weight = 11897.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.106887 restraints weight = 7780.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.108154 restraints weight = 5740.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.109219 restraints weight = 4680.850| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6763 Z= 0.157 Angle : 0.721 9.228 9192 Z= 0.363 Chirality : 0.049 0.339 968 Planarity : 0.005 0.070 1168 Dihedral : 8.882 101.667 1016 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.22 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.11 (0.29), residues: 786 helix: -0.09 (0.25), residues: 401 sheet: 0.07 (0.93), residues: 30 loop : -1.53 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 176 TYR 0.040 0.002 TYR A 453 PHE 0.019 0.002 PHE A 437 TRP 0.025 0.002 TRP A 270 HIS 0.005 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 6752) covalent geometry : angle 0.70901 / 0.36 ( 9164) SS BOND : bond 0.00213 / 0.10 ( 5) SS BOND : angle 1.52372 / 0.84 ( 10) hydrogen bonds : bond 0.04328 / 2.89 ( 299) hydrogen bonds : angle 5.18868 / 3.63 ( 864) link_NAG-ASN : bond 0.01019 / 0.66 ( 6) link_NAG-ASN : angle 2.93084 / 2.55 ( 18) *********************** 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 136 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.240 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: 0.7884 (mtmt) cc_final: 0.7518 (mtpt) REVERT: B 499 THR cc_start: 0.8571 (p) cc_final: 0.8268 (p) REVERT: A 79 MET cc_start: 0.8826 (tpp) cc_final: 0.8323 (tpp) REVERT: A 151 MET cc_start: 0.6722 (tpt) cc_final: 0.5837 (tpp) REVERT: A 248 MET cc_start: 0.7285 (ptm) cc_final: 0.6985 (ppp) REVERT: A 322 MET cc_start: 0.8340 (mmm) cc_final: 0.7265 (mmt) REVERT: A 440 LYS cc_start: 0.8057 (tmtt) cc_final: 0.7831 (ttpt) REVERT: A 453 TYR cc_start: 0.5990 (m-80) cc_final: 0.5702 (m-80) REVERT: A 455 LEU cc_start: 0.9596 (mt) cc_final: 0.9328 (mt) REVERT: A 458 TRP cc_start: 0.7159 (m100) cc_final: 0.6554 (m100) REVERT: A 479 MET cc_start: 0.8911 (ppp) cc_final: 0.8697 (ppp) REVERT: A 557 LEU cc_start: 0.8953 (mt) cc_final: 0.8545 (mt) REVERT: A 567 LEU cc_start: 0.9018 (tp) cc_final: 0.8774 (tp) REVERT: A 588 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7858 (mm-30) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0679 time to fit residues: 12.5314 Evaluate side-chains 97 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 GLN A 551 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.123736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.099999 restraints weight = 21388.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.103212 restraints weight = 11728.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.105391 restraints weight = 7582.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.106738 restraints weight = 5516.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.107790 restraints weight = 4419.646| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6763 Z= 0.158 Angle : 0.719 9.776 9192 Z= 0.359 Chirality : 0.049 0.351 968 Planarity : 0.004 0.049 1168 Dihedral : 8.506 96.421 1016 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.03 (0.29), residues: 786 helix: -0.08 (0.25), residues: 407 sheet: -0.23 (0.86), residues: 31 loop : -1.40 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 305 TYR 0.034 0.002 TYR A 453 PHE 0.021 0.002 PHE A 437 TRP 0.040 0.002 TRP B 353 HIS 0.006 0.001 HIS A 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 6752) covalent geometry : angle 0.70603 / 0.36 ( 9164) SS BOND : bond 0.00425 / 0.22 ( 5) SS BOND : angle 1.52708 / 0.78 ( 10) hydrogen bonds : bond 0.04157 / 2.82 ( 299) hydrogen bonds : angle 5.11878 / 3.60 ( 864) link_NAG-ASN : bond 0.00647 / 0.41 ( 6) link_NAG-ASN : angle 2.98247 / 2.64 ( 18) *********************** 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 127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 LYS cc_start: 0.7872 (mtmt) cc_final: 0.7458 (mtpt) REVERT: B 499 THR cc_start: 0.8501 (p) cc_final: 0.8223 (p) REVERT: A 246 LYS cc_start: 0.6273 (mttt) cc_final: 0.6071 (mttt) REVERT: A 248 MET cc_start: 0.7417 (ptm) cc_final: 0.7130 (ppp) REVERT: A 305 ARG cc_start: 0.8050 (ttp-110) cc_final: 0.7767 (ttt90) REVERT: A 382 MET cc_start: 0.8993 (mtp) cc_final: 0.8687 (mtm) REVERT: A 453 TYR cc_start: 0.5546 (m-80) cc_final: 0.4894 (m-80) REVERT: A 455 LEU cc_start: 0.9562 (mt) cc_final: 0.9326 (mt) REVERT: A 458 TRP cc_start: 0.7235 (m100) cc_final: 0.6923 (m100) REVERT: A 515 TYR cc_start: 0.7599 (t80) cc_final: 0.7394 (t80) REVERT: A 557 LEU cc_start: 0.9009 (mt) cc_final: 0.8578 (mt) REVERT: A 567 LEU cc_start: 0.9043 (tp) cc_final: 0.8839 (tp) REVERT: A 588 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7893 (mm-30) REVERT: A 594 LEU cc_start: 0.7645 (mt) cc_final: 0.7429 (mt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0657 time to fit residues: 11.5751 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 : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 67 optimal weight: 0.0670 chunk 37 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 GLN ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.124537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.100750 restraints weight = 21503.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.104078 restraints weight = 11564.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.106306 restraints weight = 7357.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.107629 restraints weight = 5297.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.108755 restraints weight = 4251.617| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6763 Z= 0.141 Angle : 0.701 9.713 9192 Z= 0.349 Chirality : 0.048 0.356 968 Planarity : 0.004 0.047 1168 Dihedral : 7.951 89.003 1016 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.77 (0.29), residues: 786 helix: 0.12 (0.26), residues: 401 sheet: -0.52 (0.90), residues: 29 loop : -1.17 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.036 0.002 TYR A 50 PHE 0.025 0.002 PHE B 456 TRP 0.036 0.002 TRP B 353 HIS 0.006 0.001 HIS A 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 6752) covalent geometry : angle 0.68940 / 0.35 ( 9164) SS BOND : bond 0.00244 / 0.12 ( 5) SS BOND : angle 1.22398 / 0.63 ( 10) hydrogen bonds : bond 0.04031 / 2.75 ( 299) hydrogen bonds : angle 5.18455 / 3.65 ( 864) link_NAG-ASN : bond 0.00595 / 0.36 ( 6) link_NAG-ASN : angle 2.87822 / 2.58 ( 18) *********************** 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: 0 poor density : 139 time to evaluate : 0.241 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: 0.7779 (mtmt) cc_final: 0.7434 (mtpt) REVERT: B 499 THR cc_start: 0.8545 (p) cc_final: 0.8245 (p) REVERT: A 151 MET cc_start: 0.6413 (tpt) cc_final: 0.5593 (tpp) REVERT: A 248 MET cc_start: 0.7364 (ptm) cc_final: 0.7099 (ppp) REVERT: A 302 ASP cc_start: 0.8128 (t0) cc_final: 0.7458 (t70) REVERT: A 305 ARG cc_start: 0.8159 (ttp-110) cc_final: 0.7941 (mtm-85) REVERT: A 440 LYS cc_start: 0.8198 (tmtt) cc_final: 0.7919 (mmtm) REVERT: A 446 VAL cc_start: 0.8724 (m) cc_final: 0.8411 (p) REVERT: A 451 PHE cc_start: 0.9058 (t80) cc_final: 0.8786 (t80) REVERT: A 453 TYR cc_start: 0.5399 (m-80) cc_final: 0.4792 (m-80) REVERT: A 455 LEU cc_start: 0.9606 (mt) cc_final: 0.9321 (mt) REVERT: A 557 LEU cc_start: 0.9077 (mt) cc_final: 0.8630 (mt) REVERT: A 567 LEU cc_start: 0.9083 (tp) cc_final: 0.8881 (tp) REVERT: A 588 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7886 (mm-30) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.0773 time to fit residues: 14.4058 Evaluate side-chains 96 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN A 42 GLN ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.124738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.100817 restraints weight = 21402.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.104077 restraints weight = 11661.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.106257 restraints weight = 7517.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.107536 restraints weight = 5488.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.108632 restraints weight = 4448.482| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6763 Z= 0.152 Angle : 0.740 9.964 9192 Z= 0.369 Chirality : 0.050 0.493 968 Planarity : 0.004 0.047 1168 Dihedral : 7.799 86.605 1016 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.22 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % 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 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: -0.77 (0.30), residues: 786 helix: 0.04 (0.26), residues: 401 sheet: -0.36 (0.91), residues: 29 loop : -1.08 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.042 0.002 TYR A 50 PHE 0.021 0.002 PHE A 229 TRP 0.037 0.002 TRP B 353 HIS 0.006 0.001 HIS A 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6752) covalent geometry : angle 0.72333 / 0.36 ( 9164) SS BOND : bond 0.00269 / 0.16 ( 5) SS BOND : angle 1.07871 / 0.54 ( 10) hydrogen bonds : bond 0.04107 / 2.80 ( 299) hydrogen bonds : angle 5.16638 / 3.63 ( 864) link_NAG-ASN : bond 0.00581 / 0.34 ( 6) link_NAG-ASN : angle 3.60206 / 2.82 ( 18) *********************** 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: 0 poor density : 137 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 LYS cc_start: 0.7758 (mtmt) cc_final: 0.7501 (mtpt) REVERT: B 499 THR cc_start: 0.8520 (p) cc_final: 0.8232 (p) REVERT: A 144 GLU cc_start: 0.8950 (mp0) cc_final: 0.8733 (mp0) REVERT: A 151 MET cc_start: 0.6408 (tpt) cc_final: 0.6188 (tpp) REVERT: A 248 MET cc_start: 0.7395 (ptm) cc_final: 0.7150 (ppp) REVERT: A 274 TRP cc_start: 0.8188 (m-10) cc_final: 0.7908 (m-10) REVERT: A 322 MET cc_start: 0.8317 (mmm) cc_final: 0.7851 (mmm) REVERT: A 407 MET cc_start: 0.9218 (mmt) cc_final: 0.8949 (mmt) REVERT: A 440 LYS cc_start: 0.8206 (tmtt) cc_final: 0.7911 (mmtm) REVERT: A 446 VAL cc_start: 0.8810 (m) cc_final: 0.8502 (p) REVERT: A 453 TYR cc_start: 0.4948 (m-80) cc_final: 0.4612 (m-80) REVERT: A 458 TRP cc_start: 0.7179 (m100) cc_final: 0.6919 (m100) REVERT: A 557 LEU cc_start: 0.9064 (mt) cc_final: 0.8645 (mt) REVERT: A 567 LEU cc_start: 0.9071 (tp) cc_final: 0.8862 (tp) REVERT: A 588 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7930 (mm-30) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0764 time to fit residues: 14.1763 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 : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.121490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.097431 restraints weight = 20640.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.100677 restraints weight = 11425.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.102927 restraints weight = 7406.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.104428 restraints weight = 5378.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.105294 restraints weight = 4292.578| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6763 Z= 0.160 Angle : 0.753 11.703 9192 Z= 0.373 Chirality : 0.050 0.402 968 Planarity : 0.004 0.046 1168 Dihedral : 7.306 70.249 1016 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.85 (0.30), residues: 786 helix: -0.07 (0.25), residues: 410 sheet: -0.63 (0.93), residues: 30 loop : -1.06 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 244 TYR 0.048 0.002 TYR A 50 PHE 0.020 0.002 PHE A 229 TRP 0.035 0.002 TRP B 353 HIS 0.006 0.001 HIS A 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 6752) covalent geometry : angle 0.73981 / 0.37 ( 9164) SS BOND : bond 0.00288 / 0.14 ( 5) SS BOND : angle 1.04791 / 0.53 ( 10) hydrogen bonds : bond 0.04288 / 2.86 ( 299) hydrogen bonds : angle 5.24258 / 3.70 ( 864) link_NAG-ASN : bond 0.00591 / 0.34 ( 6) link_NAG-ASN : angle 3.19564 / 2.67 ( 18) *********************** 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 133 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7517 (mtpt) REVERT: B 499 THR cc_start: 0.8469 (p) cc_final: 0.8168 (p) REVERT: A 151 MET cc_start: 0.6847 (tpt) cc_final: 0.6001 (tpp) REVERT: A 248 MET cc_start: 0.7451 (ptm) cc_final: 0.7216 (ppp) REVERT: A 274 TRP cc_start: 0.8128 (m-10) cc_final: 0.7882 (m-10) REVERT: A 302 ASP cc_start: 0.8127 (t0) cc_final: 0.7684 (t70) REVERT: A 440 LYS cc_start: 0.8275 (tmtt) cc_final: 0.7991 (ttpt) REVERT: A 446 VAL cc_start: 0.8891 (m) cc_final: 0.8676 (p) REVERT: A 451 PHE cc_start: 0.9111 (t80) cc_final: 0.8907 (t80) REVERT: A 453 TYR cc_start: 0.4867 (m-80) cc_final: 0.4589 (m-80) REVERT: A 458 TRP cc_start: 0.7133 (m100) cc_final: 0.6880 (m100) REVERT: A 557 LEU cc_start: 0.9097 (mt) cc_final: 0.8757 (mt) REVERT: A 567 LEU cc_start: 0.9075 (tp) cc_final: 0.8874 (tp) REVERT: A 588 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8011 (mm-30) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0613 time to fit residues: 11.6190 Evaluate side-chains 96 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 49 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.124087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.099980 restraints weight = 21534.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.103137 restraints weight = 11713.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.105168 restraints weight = 7593.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.106695 restraints weight = 5572.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.107538 restraints weight = 4466.404| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6763 Z= 0.145 Angle : 0.740 10.861 9192 Z= 0.365 Chirality : 0.049 0.390 968 Planarity : 0.004 0.048 1168 Dihedral : 6.747 54.644 1016 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % 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 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: -0.70 (0.29), residues: 786 helix: 0.12 (0.25), residues: 399 sheet: -0.65 (0.94), residues: 30 loop : -1.05 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.038 0.002 TYR A 50 PHE 0.019 0.002 PHE A 32 TRP 0.032 0.002 TRP B 353 HIS 0.005 0.001 HIS A 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 6752) covalent geometry : angle 0.72270 / 0.36 ( 9164) SS BOND : bond 0.00283 / 0.15 ( 5) SS BOND : angle 1.61602 / 0.81 ( 10) hydrogen bonds : bond 0.04009 / 2.74 ( 299) hydrogen bonds : angle 5.08929 / 3.58 ( 864) link_NAG-ASN : bond 0.00627 / 0.35 ( 6) link_NAG-ASN : angle 3.45859 / 2.84 ( 18) *********************** 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 133 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7600 (mtpt) REVERT: B 499 THR cc_start: 0.8393 (p) cc_final: 0.8093 (p) REVERT: A 63 ASN cc_start: 0.8751 (m-40) cc_final: 0.8520 (m-40) REVERT: A 151 MET cc_start: 0.6981 (tpt) cc_final: 0.6101 (tpp) REVERT: A 302 ASP cc_start: 0.8112 (t0) cc_final: 0.7840 (t70) REVERT: A 359 MET cc_start: 0.8386 (ppp) cc_final: 0.7446 (ppp) REVERT: A 407 MET cc_start: 0.9242 (mmt) cc_final: 0.9001 (mmt) REVERT: A 451 PHE cc_start: 0.9115 (t80) cc_final: 0.8888 (t80) REVERT: A 453 TYR cc_start: 0.5048 (m-80) cc_final: 0.4759 (m-80) REVERT: A 458 TRP cc_start: 0.7196 (m100) cc_final: 0.6679 (m100) REVERT: A 525 HIS cc_start: 0.8179 (t70) cc_final: 0.7951 (t-90) REVERT: A 567 LEU cc_start: 0.9069 (tp) cc_final: 0.8867 (tp) REVERT: A 588 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8009 (mm-30) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0662 time to fit residues: 12.4221 Evaluate side-chains 96 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.117338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.092789 restraints weight = 20910.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.095929 restraints weight = 11412.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.098098 restraints weight = 7363.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.099403 restraints weight = 5324.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.100510 restraints weight = 4291.534| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6763 Z= 0.198 Angle : 0.842 16.066 9192 Z= 0.415 Chirality : 0.053 0.384 968 Planarity : 0.004 0.049 1168 Dihedral : 7.233 56.847 1016 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.91 (0.30), residues: 786 helix: -0.14 (0.25), residues: 408 sheet: -0.46 (1.00), residues: 30 loop : -1.08 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.060 0.002 TYR A 50 PHE 0.027 0.002 PHE A 229 TRP 0.030 0.002 TRP A 348 HIS 0.007 0.001 HIS A 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 ( 6752) covalent geometry : angle 0.80888 / 0.41 ( 9164) SS BOND : bond 0.00413 / 0.22 ( 5) SS BOND : angle 1.65865 / 0.83 ( 10) hydrogen bonds : bond 0.04332 / 3.01 ( 299) hydrogen bonds : angle 5.43537 / 3.85 ( 864) link_NAG-ASN : bond 0.00942 / 0.49 ( 6) link_NAG-ASN : angle 5.22807 / 3.94 ( 18) *********************** 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 127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.203 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: 0.7842 (mtmt) cc_final: 0.7324 (mtpt) REVERT: B 499 THR cc_start: 0.8407 (p) cc_final: 0.8098 (p) REVERT: A 64 GLU cc_start: 0.8976 (mp0) cc_final: 0.8641 (mp0) REVERT: A 151 MET cc_start: 0.6991 (tpt) cc_final: 0.6048 (tpp) REVERT: A 302 ASP cc_start: 0.8190 (t0) cc_final: 0.7811 (t70) REVERT: A 359 MET cc_start: 0.8421 (ppp) cc_final: 0.7484 (ppp) REVERT: A 458 TRP cc_start: 0.7222 (m100) cc_final: 0.6985 (m100) REVERT: A 503 PHE cc_start: 0.8915 (t80) cc_final: 0.8704 (t80) REVERT: A 522 PHE cc_start: 0.8809 (m-10) cc_final: 0.8582 (m-10) REVERT: A 557 LEU cc_start: 0.9159 (mt) cc_final: 0.8924 (mt) REVERT: A 588 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8127 (mm-30) outliers start: 2 outliers final: 0 residues processed: 127 average time/residue: 0.0679 time to fit residues: 12.2564 Evaluate side-chains 94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 0.0020 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.120238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.097016 restraints weight = 20045.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.100186 restraints weight = 10997.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.102320 restraints weight = 7039.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.103797 restraints weight = 5070.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.104616 restraints weight = 3984.377| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6763 Z= 0.152 Angle : 0.781 10.590 9192 Z= 0.388 Chirality : 0.052 0.415 968 Planarity : 0.004 0.049 1168 Dihedral : 6.922 57.610 1016 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.53 % 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 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: -0.89 (0.29), residues: 786 helix: -0.08 (0.25), residues: 406 sheet: -0.48 (0.98), residues: 30 loop : -1.12 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 392 TYR 0.044 0.002 TYR A 50 PHE 0.022 0.002 PHE A 451 TRP 0.039 0.003 TRP A 202 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 6752) covalent geometry : angle 0.75441 / 0.38 ( 9164) SS BOND : bond 0.00338 / 0.17 ( 5) SS BOND : angle 1.48817 / 0.76 ( 10) hydrogen bonds : bond 0.04055 / 2.83 ( 299) hydrogen bonds : angle 5.45219 / 3.86 ( 864) link_NAG-ASN : bond 0.00694 / 0.37 ( 6) link_NAG-ASN : angle 4.55686 / 3.47 ( 18) ********************** 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 126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 LYS cc_start: 0.7792 (mtmt) cc_final: 0.7297 (mtpt) REVERT: B 499 THR cc_start: 0.8312 (p) cc_final: 0.7997 (p) REVERT: A 63 ASN cc_start: 0.8595 (m-40) cc_final: 0.8330 (m-40) REVERT: A 64 GLU cc_start: 0.8828 (mp0) cc_final: 0.8559 (mp0) REVERT: A 151 MET cc_start: 0.7004 (tpt) cc_final: 0.6026 (tpp) REVERT: A 196 GLU cc_start: 0.8154 (tp30) cc_final: 0.7931 (tp30) REVERT: A 302 ASP cc_start: 0.8132 (t0) cc_final: 0.7690 (t70) REVERT: A 359 MET cc_start: 0.8368 (ppp) cc_final: 0.7465 (ppp) REVERT: A 407 MET cc_start: 0.9254 (mmt) cc_final: 0.8982 (mmt) REVERT: A 440 LYS cc_start: 0.8304 (tmtt) cc_final: 0.7915 (mmtm) REVERT: A 453 TYR cc_start: 0.5838 (m-10) cc_final: 0.5174 (m-10) REVERT: A 454 MET cc_start: 0.8249 (mmp) cc_final: 0.8014 (ttt) REVERT: A 458 TRP cc_start: 0.7090 (m100) cc_final: 0.6767 (m100) REVERT: A 479 MET cc_start: 0.8542 (ppp) cc_final: 0.7818 (ppp) REVERT: A 525 HIS cc_start: 0.8264 (t70) cc_final: 0.7993 (t-90) REVERT: A 557 LEU cc_start: 0.9153 (mt) cc_final: 0.8900 (mt) REVERT: A 588 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8055 (mm-30) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.0611 time to fit residues: 11.0119 Evaluate side-chains 97 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 ASN ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 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 = 0.4007 r_free = 0.4007 target = 0.116324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.091311 restraints weight = 20920.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.094414 restraints weight = 11579.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.096621 restraints weight = 7539.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.098048 restraints weight = 5489.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.098907 restraints weight = 4399.654| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6763 Z= 0.191 Angle : 0.816 11.796 9192 Z= 0.410 Chirality : 0.053 0.399 968 Planarity : 0.005 0.049 1168 Dihedral : 7.029 59.713 1016 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.15 % 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 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: -1.19 (0.29), residues: 786 helix: -0.37 (0.25), residues: 413 sheet: -0.64 (0.97), residues: 30 loop : -1.23 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 392 TYR 0.043 0.002 TYR A 50 PHE 0.023 0.002 PHE A 451 TRP 0.027 0.003 TRP A 202 HIS 0.004 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 6752) covalent geometry : angle 0.79381 / 0.40 ( 9164) SS BOND : bond 0.00436 / 0.24 ( 5) SS BOND : angle 1.71328 / 0.87 ( 10) hydrogen bonds : bond 0.04500 / 3.15 ( 299) hydrogen bonds : angle 5.66164 / 4.01 ( 864) link_NAG-ASN : bond 0.00612 / 0.34 ( 6) link_NAG-ASN : angle 4.17806 / 3.26 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1268.52 seconds wall clock time: 22 minutes 45.87 seconds (1365.87 seconds total)