Starting phenix.real_space_refine on Tue Aug 4 17:53:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wfo_65933/08_2026/9wfo_65933.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wfo_65933/08_2026/9wfo_65933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wfo_65933/08_2026/9wfo_65933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wfo_65933/08_2026/9wfo_65933.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wfo_65933/08_2026/9wfo_65933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wfo_65933/08_2026/9wfo_65933.map" } resolution = 3.31 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= 0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 26 5.16 5 C 3643 2.51 5 N 904 2.21 5 O 970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5546 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 137 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 5172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5172 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 32, 'TRANS': 612} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 7, 'GLU:plan': 5, 'ASP:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 111 Chain: "C" 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: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 209 Unusual residues: {'CLR': 1, 'MX7': 1, 'NAG': 4, 'POV': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.31, per 1000 atoms: 0.24 Number of scatterers: 5546 At special positions: 0 Unit cell: (81.18, 86.92, 105.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 3 15.00 O 970 8.00 N 904 7.00 C 3643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 450 " distance=2.03 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 BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 801 " - " ASN A 550 " " NAG A 802 " - " ASN A 459 " " NAG A 803 " - " ASN A 605 " " NAG A 808 " - " ASN A 525 " " NAG C 1 " - " ASN A 570 " Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 127.9 milliseconds 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1258 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 60.4% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid 33 through 38 removed outlier: 3.724A pdb=" N ASN B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 61 through 82 Proline residue: A 80 - end of helix Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 111 through 132 Processing helix chain 'A' and resid 134 through 153 Proline residue: A 145 - end of helix removed outlier: 3.871A pdb=" N ASP A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 158 through 174 removed outlier: 3.734A pdb=" N PHE A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.647A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 218 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.867A pdb=" N SER A 233 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TRP A 236 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU A 237 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 246 through 272 removed outlier: 4.727A pdb=" N GLY A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N PHE A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 294 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 308 through 311 Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.948A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 377 Processing helix chain 'A' and resid 378 through 383 removed outlier: 5.291A pdb=" N HIS A 381 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE A 382 " --> pdb=" O TYR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 440 through 455 Processing helix chain 'A' and resid 456 through 459 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 511 through 523 removed outlier: 4.549A pdb=" N LYS A 515 " --> pdb=" O PRO A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 657 through 675 Processing helix chain 'A' and resid 676 through 709 Processing helix chain 'A' and resid 712 through 725 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 32 removed outlier: 4.200A pdb=" N TYR A 425 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 413 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N HIS A 408 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER A 472 " --> pdb=" O HIS A 408 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS A 410 " --> pdb=" O TRP A 470 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN A 478 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL A 604 " --> pdb=" O ASN A 550 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN A 550 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.652A pdb=" N VAL A 560 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 571 " --> pdb=" O VAL A 562 " (cutoff:3.500A) 292 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 822 1.31 - 1.44: 1692 1.44 - 1.57: 3134 1.57 - 1.69: 10 1.69 - 1.82: 43 Bond restraints: 5701 Sorted by residual: bond pdb=" C39 MX7 A 805 " pdb=" C3A MX7 A 805 " ideal model delta sigma weight residual 1.332 1.559 -0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C1 NAG A 803 " pdb=" O5 NAG A 803 " ideal model delta sigma weight residual 1.406 1.525 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" C31 MX7 A 805 " pdb=" O31 MX7 A 805 " ideal model delta sigma weight residual 1.326 1.422 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C21 MX7 A 805 " pdb=" O21 MX7 A 805 " ideal model delta sigma weight residual 1.327 1.419 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C1 NAG A 801 " pdb=" O5 NAG A 801 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.08e+01 ... (remaining 5696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.45: 7680 5.45 - 10.90: 56 10.90 - 16.35: 5 16.35 - 21.80: 0 21.80 - 27.25: 2 Bond angle restraints: 7743 Sorted by residual: angle pdb=" C28 MX7 A 805 " pdb=" C29 MX7 A 805 " pdb=" C2A MX7 A 805 " ideal model delta sigma weight residual 127.42 154.67 -27.25 3.00e+00 1.11e-01 8.25e+01 angle pdb=" C29 MX7 A 805 " pdb=" C2A MX7 A 805 " pdb=" C2B MX7 A 805 " ideal model delta sigma weight residual 127.43 154.53 -27.10 3.00e+00 1.11e-01 8.16e+01 angle pdb=" C39 MX7 A 805 " pdb=" C3A MX7 A 805 " pdb=" C3B MX7 A 805 " ideal model delta sigma weight residual 128.09 111.83 16.26 3.00e+00 1.11e-01 2.94e+01 angle pdb=" C38 MX7 A 805 " pdb=" C39 MX7 A 805 " pdb=" C3A MX7 A 805 " ideal model delta sigma weight residual 128.05 112.34 15.71 3.00e+00 1.11e-01 2.74e+01 angle pdb=" N PRO A 337 " pdb=" CA PRO A 337 " pdb=" C PRO A 337 " ideal model delta sigma weight residual 111.41 118.19 -6.78 1.50e+00 4.44e-01 2.04e+01 ... (remaining 7738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.39: 3175 25.39 - 50.79: 209 50.79 - 76.18: 55 76.18 - 101.58: 15 101.58 - 126.97: 12 Dihedral angle restraints: 3466 sinusoidal: 1516 harmonic: 1950 Sorted by residual: dihedral pdb=" CD ARG A 453 " pdb=" NE ARG A 453 " pdb=" CZ ARG A 453 " pdb=" NH1 ARG A 453 " ideal model delta sinusoidal sigma weight residual 0.00 -72.21 72.21 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CD ARG A 359 " pdb=" NE ARG A 359 " pdb=" CZ ARG A 359 " pdb=" NH1 ARG A 359 " ideal model delta sinusoidal sigma weight residual 0.00 -58.08 58.08 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CA CYS A 134 " pdb=" C CYS A 134 " pdb=" N TYR A 135 " pdb=" CA TYR A 135 " ideal model delta harmonic sigma weight residual -180.00 -152.20 -27.80 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 3463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 675 0.078 - 0.157: 155 0.157 - 0.235: 16 0.235 - 0.313: 7 0.313 - 0.392: 2 Chirality restraints: 855 Sorted by residual: chirality pdb=" CG LEU A 331 " pdb=" CB LEU A 331 " pdb=" CD1 LEU A 331 " pdb=" CD2 LEU A 331 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CB THR A 551 " pdb=" CA THR A 551 " pdb=" OG1 THR A 551 " pdb=" CG2 THR A 551 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C1 NAG A 808 " pdb=" ND2 ASN A 525 " pdb=" C2 NAG A 808 " pdb=" O5 NAG A 808 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 852 not shown) Planarity restraints: 956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 MX7 A 805 " 0.168 2.00e-02 2.50e+03 3.54e-01 1.25e+03 pdb=" C39 MX7 A 805 " -0.483 2.00e-02 2.50e+03 pdb=" C3A MX7 A 805 " 0.465 2.00e-02 2.50e+03 pdb=" C3B MX7 A 805 " -0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 453 " 1.058 9.50e-02 1.11e+02 4.74e-01 1.36e+02 pdb=" NE ARG A 453 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 453 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 453 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 453 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 359 " -0.936 9.50e-02 1.11e+02 4.20e-01 1.07e+02 pdb=" NE ARG A 359 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG A 359 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 359 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 359 " -0.024 2.00e-02 2.50e+03 ... (remaining 953 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 27 2.52 - 3.12: 4204 3.12 - 3.71: 8872 3.71 - 4.31: 12314 4.31 - 4.90: 20927 Nonbonded interactions: 46344 Sorted by model distance: nonbonded pdb=" O ASP A 60 " pdb=" OH TYR A 200 " model vdw 1.929 3.040 nonbonded pdb=" O SER A 233 " pdb=" NZ LYS A 242 " model vdw 2.309 3.120 nonbonded pdb=" OD1 ASN A 192 " pdb=" NH2 ARG A 317 " model vdw 2.319 3.120 nonbonded pdb=" O PHE A 286 " pdb=" ND2 ASN A 290 " model vdw 2.337 3.120 nonbonded pdb=" N SER A 405 " pdb=" OD1 ASN A 474 " model vdw 2.341 3.120 ... (remaining 46339 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.960 Find NCS groups from input model: 0.030 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.227 5708 Z= 0.417 Angle : 1.322 27.246 7763 Z= 0.681 Chirality : 0.069 0.392 855 Planarity : 0.026 0.474 951 Dihedral : 20.143 126.973 2205 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.82 % Favored : 96.02 % Rotamer: Outliers : 1.99 % Allowed : 13.20 % Favored : 84.81 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.32), residues: 654 helix: 0.31 (0.27), residues: 330 sheet: -0.15 (0.59), residues: 68 loop : 0.23 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG A 704 TYR 0.036 0.006 TYR A 397 PHE 0.023 0.002 PHE A 73 TRP 0.036 0.003 TRP A 470 HIS 0.009 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00829 / 0.42 ( 5701) covalent geometry : angle 1.30591 / 0.68 ( 7743) SS BOND : bond 0.00031 / 0.02 ( 1) SS BOND : angle 2.58526 / 1.22 ( 2) hydrogen bonds : bond 0.14165 / 8.98 ( 292) hydrogen bonds : angle 6.91819 / 5.05 ( 819) link_BETA1-4 : bond 0.00345 / 0.18 ( 1) link_BETA1-4 : angle 1.55403 / 0.78 ( 3) link_NAG-ASN : bond 0.01168 / 0.69 ( 5) link_NAG-ASN : angle 4.84018 / 2.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 354 GLN cc_start: 0.6098 (tp40) cc_final: 0.5877 (pt0) REVERT: A 372 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7159 (tt) REVERT: A 453 ARG cc_start: 0.7625 (mtt-85) cc_final: 0.7315 (ttp-170) outliers start: 11 outliers final: 3 residues processed: 76 average time/residue: 0.0882 time to fit residues: 8.5863 Evaluate side-chains 69 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 452 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.0000 chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 HIS ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 GLN ** A 479 GLN ** 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 = 0.4348 r_free = 0.4348 target = 0.219069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.148512 restraints weight = 6179.154| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.79 r_work: 0.3460 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5708 Z= 0.145 Angle : 0.687 11.442 7763 Z= 0.320 Chirality : 0.045 0.323 855 Planarity : 0.004 0.034 951 Dihedral : 16.808 106.011 1020 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.45 % Allowed : 13.20 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.84 (0.35), residues: 654 helix: 1.62 (0.29), residues: 336 sheet: 0.31 (0.54), residues: 73 loop : 1.20 (0.46), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 453 TYR 0.013 0.001 TYR A 415 PHE 0.012 0.001 PHE A 150 TRP 0.013 0.001 TRP A 198 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 5701) covalent geometry : angle 0.66499 / 0.32 ( 7743) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.92558 / 0.42 ( 2) hydrogen bonds : bond 0.03879 / 2.52 ( 292) hydrogen bonds : angle 5.26188 / 3.83 ( 819) link_BETA1-4 : bond 0.00537 / 0.28 ( 1) link_BETA1-4 : angle 2.69227 / 1.49 ( 3) link_NAG-ASN : bond 0.00947 / 0.47 ( 5) link_NAG-ASN : angle 3.77603 / 2.29 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.172 Fit side-chains REVERT: A 200 TYR cc_start: 0.8198 (m-80) cc_final: 0.7939 (m-80) REVERT: A 354 GLN cc_start: 0.6260 (tp40) cc_final: 0.5793 (pt0) REVERT: A 372 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6604 (tt) REVERT: A 415 TYR cc_start: 0.7669 (p90) cc_final: 0.7409 (p90) REVERT: A 453 ARG cc_start: 0.7563 (mtt-85) cc_final: 0.7311 (ttp-170) REVERT: A 468 ASP cc_start: 0.7825 (t0) cc_final: 0.7495 (t70) outliers start: 8 outliers final: 4 residues processed: 74 average time/residue: 0.0701 time to fit residues: 7.0914 Evaluate side-chains 68 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 589 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 40 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 6 optimal weight: 0.1980 chunk 31 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.0070 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 HIS A 81 GLN ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 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 = 0.4346 r_free = 0.4346 target = 0.218283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.147652 restraints weight = 6100.306| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.78 r_work: 0.3303 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5708 Z= 0.125 Angle : 0.608 9.968 7763 Z= 0.281 Chirality : 0.043 0.315 855 Planarity : 0.004 0.033 951 Dihedral : 14.564 102.787 1019 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.45 % Allowed : 12.66 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.34), residues: 654 helix: 1.82 (0.29), residues: 335 sheet: 0.48 (0.57), residues: 73 loop : 1.24 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 49 TYR 0.010 0.001 TYR A 425 PHE 0.010 0.001 PHE A 150 TRP 0.013 0.001 TRP A 198 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5701) covalent geometry : angle 0.58797 / 0.28 ( 7743) SS BOND : bond 0.00164 / 0.09 ( 1) SS BOND : angle 0.77827 / 0.35 ( 2) hydrogen bonds : bond 0.03417 / 2.24 ( 292) hydrogen bonds : angle 4.91374 / 3.60 ( 819) link_BETA1-4 : bond 0.00549 / 0.29 ( 1) link_BETA1-4 : angle 3.09364 / 1.67 ( 3) link_NAG-ASN : bond 0.00892 / 0.47 ( 5) link_NAG-ASN : angle 3.32036 / 1.91 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8181 (m-80) cc_final: 0.7934 (m-80) REVERT: A 354 GLN cc_start: 0.6280 (tp40) cc_final: 0.5643 (pt0) REVERT: A 453 ARG cc_start: 0.7488 (mtt-85) cc_final: 0.7268 (ttp-170) REVERT: A 468 ASP cc_start: 0.7632 (t0) cc_final: 0.7275 (t0) REVERT: A 579 MET cc_start: 0.3681 (OUTLIER) cc_final: 0.1437 (mmt) outliers start: 8 outliers final: 4 residues processed: 82 average time/residue: 0.0686 time to fit residues: 7.5849 Evaluate side-chains 76 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 579 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 15 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 30.0000 chunk 4 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 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 = 0.4329 r_free = 0.4329 target = 0.216250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145295 restraints weight = 6159.906| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.80 r_work: 0.3425 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5708 Z= 0.140 Angle : 0.623 11.288 7763 Z= 0.285 Chirality : 0.042 0.310 855 Planarity : 0.004 0.044 951 Dihedral : 13.168 100.059 1016 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.45 % Allowed : 14.65 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.00 (0.34), residues: 654 helix: 1.80 (0.29), residues: 335 sheet: 0.60 (0.58), residues: 73 loop : 1.10 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 513 TYR 0.012 0.001 TYR A 415 PHE 0.011 0.001 PHE A 150 TRP 0.012 0.001 TRP A 198 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 5701) covalent geometry : angle 0.59824 / 0.28 ( 7743) SS BOND : bond 0.00166 / 0.09 ( 1) SS BOND : angle 0.72348 / 0.36 ( 2) hydrogen bonds : bond 0.03271 / 2.16 ( 292) hydrogen bonds : angle 4.79024 / 3.52 ( 819) link_BETA1-4 : bond 0.00425 / 0.22 ( 1) link_BETA1-4 : angle 3.58025 / 1.95 ( 3) link_NAG-ASN : bond 0.00782 / 0.38 ( 5) link_NAG-ASN : angle 3.70116 / 2.15 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.199 Fit side-chains REVERT: A 200 TYR cc_start: 0.8273 (m-80) cc_final: 0.8014 (m-80) REVERT: A 354 GLN cc_start: 0.6482 (tp40) cc_final: 0.5769 (pt0) REVERT: A 415 TYR cc_start: 0.8007 (p90) cc_final: 0.7759 (p90) REVERT: A 453 ARG cc_start: 0.7545 (mtt-85) cc_final: 0.7314 (ttp-170) REVERT: A 468 ASP cc_start: 0.7735 (t0) cc_final: 0.7378 (t0) REVERT: A 579 MET cc_start: 0.3756 (OUTLIER) cc_final: 0.1487 (mmt) REVERT: A 598 CYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6831 (t) outliers start: 8 outliers final: 3 residues processed: 78 average time/residue: 0.0689 time to fit residues: 7.3516 Evaluate side-chains 74 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 598 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 8.9990 chunk 35 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 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 = 0.4265 r_free = 0.4265 target = 0.209146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.136811 restraints weight = 6326.364| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.81 r_work: 0.3372 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5708 Z= 0.186 Angle : 0.649 10.102 7763 Z= 0.301 Chirality : 0.043 0.306 855 Planarity : 0.005 0.065 951 Dihedral : 11.748 94.726 1012 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.45 % Allowed : 16.27 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.85 (0.34), residues: 654 helix: 1.67 (0.29), residues: 333 sheet: 0.63 (0.60), residues: 72 loop : 1.01 (0.45), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 513 TYR 0.010 0.001 TYR A 116 PHE 0.016 0.001 PHE A 150 TRP 0.012 0.001 TRP A 198 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 5701) covalent geometry : angle 0.61890 / 0.29 ( 7743) SS BOND : bond 0.00324 / 0.17 ( 1) SS BOND : angle 0.92035 / 0.44 ( 2) hydrogen bonds : bond 0.03434 / 2.28 ( 292) hydrogen bonds : angle 4.84931 / 3.56 ( 819) link_BETA1-4 : bond 0.00091 / 0.05 ( 1) link_BETA1-4 : angle 4.39144 / 2.39 ( 3) link_NAG-ASN : bond 0.00743 / 0.36 ( 5) link_NAG-ASN : angle 4.00659 / 2.19 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 ASN cc_start: 0.8245 (t0) cc_final: 0.6985 (p0) REVERT: A 200 TYR cc_start: 0.8310 (m-80) cc_final: 0.8066 (m-80) REVERT: A 354 GLN cc_start: 0.6617 (tp40) cc_final: 0.5572 (pt0) REVERT: A 415 TYR cc_start: 0.8107 (p90) cc_final: 0.7760 (p90) REVERT: A 453 ARG cc_start: 0.7588 (mtt-85) cc_final: 0.7271 (ttp-170) REVERT: A 468 ASP cc_start: 0.7906 (t0) cc_final: 0.7650 (t0) REVERT: A 579 MET cc_start: 0.3966 (OUTLIER) cc_final: 0.1623 (mmt) REVERT: A 598 CYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7028 (t) outliers start: 8 outliers final: 5 residues processed: 76 average time/residue: 0.0782 time to fit residues: 7.8742 Evaluate side-chains 74 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 459 ASN Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 598 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 57 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 HIS ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 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 = 0.4284 r_free = 0.4284 target = 0.211358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.145029 restraints weight = 6265.102| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.11 r_work: 0.3406 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5708 Z= 0.133 Angle : 0.605 10.046 7763 Z= 0.279 Chirality : 0.041 0.305 855 Planarity : 0.004 0.037 951 Dihedral : 10.846 91.349 1012 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.35 % Allowed : 16.64 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.04 (0.35), residues: 654 helix: 1.79 (0.29), residues: 334 sheet: 0.64 (0.57), residues: 78 loop : 1.20 (0.46), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 513 TYR 0.010 0.001 TYR A 415 PHE 0.012 0.001 PHE A 67 TRP 0.013 0.001 TRP A 198 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 5701) covalent geometry : angle 0.57476 / 0.27 ( 7743) SS BOND : bond 0.00239 / 0.13 ( 1) SS BOND : angle 0.66817 / 0.32 ( 2) hydrogen bonds : bond 0.03166 / 2.12 ( 292) hydrogen bonds : angle 4.76443 / 3.49 ( 819) link_BETA1-4 : bond 0.00285 / 0.15 ( 1) link_BETA1-4 : angle 4.63719 / 2.50 ( 3) link_NAG-ASN : bond 0.00764 / 0.37 ( 5) link_NAG-ASN : angle 3.81134 / 2.13 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: B 36 ASN cc_start: 0.8196 (t0) cc_final: 0.7002 (p0) REVERT: A 200 TYR cc_start: 0.8250 (m-80) cc_final: 0.8026 (m-80) REVERT: A 354 GLN cc_start: 0.6733 (tp40) cc_final: 0.5551 (pt0) REVERT: A 415 TYR cc_start: 0.8171 (p90) cc_final: 0.7923 (p90) REVERT: A 453 ARG cc_start: 0.7567 (mtt-85) cc_final: 0.7280 (ttp-170) REVERT: A 579 MET cc_start: 0.3869 (OUTLIER) cc_final: 0.1581 (mmt) REVERT: A 598 CYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7003 (t) outliers start: 13 outliers final: 8 residues processed: 76 average time/residue: 0.0726 time to fit residues: 7.3832 Evaluate side-chains 77 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 598 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 HIS ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.210153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.144305 restraints weight = 6316.720| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.25 r_work: 0.3344 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5708 Z= 0.204 Angle : 0.635 10.738 7763 Z= 0.300 Chirality : 0.043 0.302 855 Planarity : 0.005 0.039 951 Dihedral : 10.733 86.339 1012 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.35 % Allowed : 17.36 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.82 (0.35), residues: 654 helix: 1.63 (0.29), residues: 332 sheet: 0.59 (0.57), residues: 78 loop : 1.04 (0.46), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 513 TYR 0.010 0.001 TYR A 415 PHE 0.015 0.001 PHE A 150 TRP 0.012 0.002 TRP A 147 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 ( 5701) covalent geometry : angle 0.61081 / 0.29 ( 7743) SS BOND : bond 0.00262 / 0.14 ( 1) SS BOND : angle 0.79993 / 0.39 ( 2) hydrogen bonds : bond 0.03424 / 2.27 ( 292) hydrogen bonds : angle 4.84876 / 3.57 ( 819) link_BETA1-4 : bond 0.00207 / 0.11 ( 1) link_BETA1-4 : angle 3.56121 / 1.81 ( 3) link_NAG-ASN : bond 0.00713 / 0.34 ( 5) link_NAG-ASN : angle 3.71322 / 2.08 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: B 36 ASN cc_start: 0.8209 (t0) cc_final: 0.7014 (p0) REVERT: A 200 TYR cc_start: 0.8329 (m-80) cc_final: 0.8064 (m-80) REVERT: A 354 GLN cc_start: 0.6927 (tp40) cc_final: 0.5514 (pt0) REVERT: A 415 TYR cc_start: 0.8297 (p90) cc_final: 0.8017 (p90) REVERT: A 453 ARG cc_start: 0.7615 (mtt-85) cc_final: 0.7310 (ttp-170) REVERT: A 468 ASP cc_start: 0.7962 (t0) cc_final: 0.7685 (t0) REVERT: A 509 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7495 (mm) REVERT: A 579 MET cc_start: 0.3933 (OUTLIER) cc_final: 0.1613 (mmt) REVERT: A 598 CYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7120 (t) outliers start: 13 outliers final: 10 residues processed: 81 average time/residue: 0.0742 time to fit residues: 7.8968 Evaluate side-chains 82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 598 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 41 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 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 = 0.4313 r_free = 0.4313 target = 0.214021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.143783 restraints weight = 6263.391| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.83 r_work: 0.3341 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5708 Z= 0.122 Angle : 0.588 11.210 7763 Z= 0.275 Chirality : 0.040 0.303 855 Planarity : 0.004 0.037 951 Dihedral : 10.096 80.396 1012 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.53 % Allowed : 16.82 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.98 (0.35), residues: 654 helix: 1.81 (0.29), residues: 334 sheet: 0.64 (0.56), residues: 79 loop : 1.05 (0.46), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 513 TYR 0.011 0.001 TYR A 415 PHE 0.012 0.001 PHE A 67 TRP 0.014 0.001 TRP A 147 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 5701) covalent geometry : angle 0.56413 / 0.27 ( 7743) SS BOND : bond 0.00168 / 0.09 ( 1) SS BOND : angle 0.64340 / 0.33 ( 2) hydrogen bonds : bond 0.03137 / 2.10 ( 292) hydrogen bonds : angle 4.71755 / 3.46 ( 819) link_BETA1-4 : bond 0.00006 / 0.00 ( 1) link_BETA1-4 : angle 2.81459 / 1.47 ( 3) link_NAG-ASN : bond 0.00767 / 0.37 ( 5) link_NAG-ASN : angle 3.56690 / 1.97 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 ASN cc_start: 0.8150 (t0) cc_final: 0.7011 (p0) REVERT: A 187 ASN cc_start: 0.5550 (m-40) cc_final: 0.5339 (m-40) REVERT: A 200 TYR cc_start: 0.8243 (m-80) cc_final: 0.8017 (m-80) REVERT: A 354 GLN cc_start: 0.6837 (tp40) cc_final: 0.5341 (pt0) REVERT: A 415 TYR cc_start: 0.8257 (p90) cc_final: 0.7980 (p90) REVERT: A 453 ARG cc_start: 0.7561 (mtt-85) cc_final: 0.7222 (ttp-170) REVERT: A 509 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7496 (mm) REVERT: A 578 LYS cc_start: 0.7751 (mmtp) cc_final: 0.7361 (mmtp) REVERT: A 579 MET cc_start: 0.3774 (OUTLIER) cc_final: 0.1604 (mmt) REVERT: A 598 CYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7132 (t) outliers start: 14 outliers final: 9 residues processed: 77 average time/residue: 0.0681 time to fit residues: 7.1203 Evaluate side-chains 78 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 459 ASN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 598 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.0170 chunk 47 optimal weight: 0.0980 chunk 20 optimal weight: 0.2980 chunk 58 optimal weight: 30.0000 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 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 = 0.4317 r_free = 0.4317 target = 0.214458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143901 restraints weight = 6278.016| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.85 r_work: 0.3301 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5708 Z= 0.110 Angle : 0.582 11.563 7763 Z= 0.268 Chirality : 0.039 0.303 855 Planarity : 0.004 0.038 951 Dihedral : 9.046 82.801 1012 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.99 % Allowed : 17.72 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.19 (0.35), residues: 654 helix: 2.00 (0.29), residues: 333 sheet: 0.83 (0.58), residues: 79 loop : 1.10 (0.46), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 513 TYR 0.011 0.001 TYR A 415 PHE 0.010 0.001 PHE A 67 TRP 0.013 0.001 TRP A 198 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 5701) covalent geometry : angle 0.55476 / 0.26 ( 7743) SS BOND : bond 0.00183 / 0.10 ( 1) SS BOND : angle 0.57523 / 0.31 ( 2) hydrogen bonds : bond 0.02996 / 2.03 ( 292) hydrogen bonds : angle 4.60448 / 3.38 ( 819) link_BETA1-4 : bond 0.00050 / 0.03 ( 1) link_BETA1-4 : angle 2.54667 / 1.32 ( 3) link_NAG-ASN : bond 0.00772 / 0.37 ( 5) link_NAG-ASN : angle 3.85968 / 2.14 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: B 36 ASN cc_start: 0.8038 (t0) cc_final: 0.6947 (p0) REVERT: A 200 TYR cc_start: 0.8203 (m-80) cc_final: 0.7966 (m-80) REVERT: A 354 GLN cc_start: 0.6780 (tp40) cc_final: 0.6552 (tp-100) REVERT: A 415 TYR cc_start: 0.8241 (p90) cc_final: 0.7989 (p90) REVERT: A 453 ARG cc_start: 0.7527 (mtt-85) cc_final: 0.7166 (ttp-170) REVERT: A 509 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7482 (mm) REVERT: A 578 LYS cc_start: 0.7745 (mmtp) cc_final: 0.7301 (mmtp) REVERT: A 579 MET cc_start: 0.3675 (OUTLIER) cc_final: 0.1460 (mmt) REVERT: A 598 CYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7108 (t) outliers start: 11 outliers final: 6 residues processed: 77 average time/residue: 0.0752 time to fit residues: 7.8324 Evaluate side-chains 79 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 598 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 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 = 0.4306 r_free = 0.4306 target = 0.213004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.142374 restraints weight = 6399.884| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.85 r_work: 0.3318 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5708 Z= 0.136 Angle : 0.580 8.570 7763 Z= 0.273 Chirality : 0.039 0.302 855 Planarity : 0.004 0.037 951 Dihedral : 8.686 83.257 1012 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.99 % Allowed : 17.54 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.18 (0.35), residues: 654 helix: 1.99 (0.29), residues: 332 sheet: 0.86 (0.58), residues: 79 loop : 1.07 (0.47), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 513 TYR 0.016 0.001 TYR A 164 PHE 0.011 0.001 PHE A 67 TRP 0.012 0.001 TRP A 147 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 5701) covalent geometry : angle 0.55432 / 0.27 ( 7743) SS BOND : bond 0.00230 / 0.12 ( 1) SS BOND : angle 0.81673 / 0.48 ( 2) hydrogen bonds : bond 0.03116 / 2.09 ( 292) hydrogen bonds : angle 4.61816 / 3.41 ( 819) link_BETA1-4 : bond 0.00479 / 0.25 ( 1) link_BETA1-4 : angle 1.88846 / 1.00 ( 3) link_NAG-ASN : bond 0.00741 / 0.36 ( 5) link_NAG-ASN : angle 3.83993 / 2.06 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: B 36 ASN cc_start: 0.8037 (t0) cc_final: 0.6934 (p0) REVERT: A 200 TYR cc_start: 0.8265 (m-80) cc_final: 0.8019 (m-80) REVERT: A 354 GLN cc_start: 0.6933 (tp40) cc_final: 0.6677 (tp-100) REVERT: A 415 TYR cc_start: 0.8310 (p90) cc_final: 0.8063 (p90) REVERT: A 453 ARG cc_start: 0.7567 (mtt-85) cc_final: 0.7215 (ttp-170) REVERT: A 509 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7510 (mm) REVERT: A 579 MET cc_start: 0.3766 (OUTLIER) cc_final: 0.1541 (mmt) REVERT: A 598 CYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7139 (t) outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 0.0742 time to fit residues: 7.6886 Evaluate side-chains 80 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 598 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 64 optimal weight: 0.0060 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 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 = 0.4305 r_free = 0.4305 target = 0.212861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.142508 restraints weight = 6285.782| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.82 r_work: 0.3320 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5708 Z= 0.144 Angle : 0.576 8.205 7763 Z= 0.274 Chirality : 0.040 0.303 855 Planarity : 0.004 0.038 951 Dihedral : 8.476 81.779 1012 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.17 % Allowed : 17.72 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.12 (0.35), residues: 654 helix: 1.94 (0.29), residues: 332 sheet: 0.91 (0.59), residues: 79 loop : 1.02 (0.47), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 513 TYR 0.017 0.001 TYR A 164 PHE 0.011 0.001 PHE A 67 TRP 0.016 0.001 TRP A 147 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 5701) covalent geometry : angle 0.55679 / 0.27 ( 7743) SS BOND : bond 0.00237 / 0.12 ( 1) SS BOND : angle 0.69557 / 0.36 ( 2) hydrogen bonds : bond 0.03144 / 2.11 ( 292) hydrogen bonds : angle 4.66028 / 3.44 ( 819) link_BETA1-4 : bond 0.00060 / 0.03 ( 1) link_BETA1-4 : angle 1.83473 / 1.06 ( 3) link_NAG-ASN : bond 0.00731 / 0.35 ( 5) link_NAG-ASN : angle 3.34590 / 1.77 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1537.00 seconds wall clock time: 27 minutes 0.84 seconds (1620.84 seconds total)