Starting phenix.real_space_refine on Fri Aug 22 14:36:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6l_36922/08_2025/8k6l_36922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6l_36922/08_2025/8k6l_36922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k6l_36922/08_2025/8k6l_36922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6l_36922/08_2025/8k6l_36922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k6l_36922/08_2025/8k6l_36922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6l_36922/08_2025/8k6l_36922.map" } resolution = 2.92 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= 0.092 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 S 34 5.16 5 Cl 2 4.86 5 C 2749 2.51 5 N 651 2.21 5 O 719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4155 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4086 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 18, 'TRANS': 528} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 3, 'TYR:plan': 4, 'GLU:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 8, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 109 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: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'IOQ': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.24, per 1000 atoms: 0.30 Number of scatterers: 4155 At special positions: 0 Unit cell: (65.24, 100.656, 87.608, 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) Cl 2 17.00 S 34 16.00 O 719 8.00 N 651 7.00 C 2749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.04 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=1.71 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " 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 B 1 " - " NAG B 2 " NAG-ASN " NAG A 802 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 147.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 996 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 3 sheets defined 67.3% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 26 through 51 removed outlier: 3.662A pdb=" N PHE A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 33 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 71 through 88 removed outlier: 3.577A pdb=" N ILE A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 92 through 111 removed outlier: 3.808A pdb=" N THR A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 removed outlier: 4.173A pdb=" N PHE A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.747A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 4.516A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.844A pdb=" N ILE A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 228 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 removed outlier: 3.614A pdb=" N LEU A 263 " --> pdb=" O TRP A 259 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.851A pdb=" N PHE A 276 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.810A pdb=" N ILE A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 367 removed outlier: 5.301A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 401 removed outlier: 3.630A pdb=" N GLY A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.514A pdb=" N ILE A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 423 removed outlier: 3.876A pdb=" N PHE A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 527 through 550 removed outlier: 3.846A pdb=" N THR A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 560 Processing helix chain 'A' and resid 567 through 583 Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 617 through 651 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 502 removed outlier: 3.594A pdb=" N PHE A 501 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 602 removed outlier: 6.820A pdb=" N CYS A 599 " --> pdb=" O TYR A 616 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR A 616 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS A 601 " --> pdb=" O ARG A 614 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 711 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: 0.62 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 881 1.33 - 1.45: 1009 1.45 - 1.57: 2315 1.57 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 4258 Sorted by residual: bond pdb=" C THR A 186 " pdb=" N PRO A 187 " ideal model delta sigma weight residual 1.331 1.371 -0.039 7.90e-03 1.60e+04 2.44e+01 bond pdb=" C SER A 140 " pdb=" N THR A 141 " ideal model delta sigma weight residual 1.332 1.291 0.041 1.40e-02 5.10e+03 8.70e+00 bond pdb=" C PHE A 591 " pdb=" O PHE A 591 " ideal model delta sigma weight residual 1.237 1.210 0.026 1.17e-02 7.31e+03 5.05e+00 bond pdb=" C PRO A 588 " pdb=" O PRO A 588 " ideal model delta sigma weight residual 1.237 1.211 0.026 1.16e-02 7.43e+03 4.98e+00 bond pdb=" C ILE A 589 " pdb=" O ILE A 589 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.13e-02 7.83e+03 4.97e+00 ... (remaining 4253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 5574 2.40 - 4.79: 175 4.79 - 7.19: 21 7.19 - 9.59: 10 9.59 - 11.98: 2 Bond angle restraints: 5782 Sorted by residual: angle pdb=" C ILE A 585 " pdb=" CA ILE A 585 " pdb=" CB ILE A 585 " ideal model delta sigma weight residual 111.30 101.87 9.43 9.60e-01 1.09e+00 9.65e+01 angle pdb=" N ILE A 52 " pdb=" CA ILE A 52 " pdb=" C ILE A 52 " ideal model delta sigma weight residual 110.62 117.58 -6.96 1.02e+00 9.61e-01 4.65e+01 angle pdb=" N ASN A 375 " pdb=" CA ASN A 375 " pdb=" C ASN A 375 " ideal model delta sigma weight residual 111.02 120.98 -9.96 1.52e+00 4.33e-01 4.30e+01 angle pdb=" C ALA A 32 " pdb=" N ALA A 33 " pdb=" CA ALA A 33 " ideal model delta sigma weight residual 120.28 129.02 -8.74 1.34e+00 5.57e-01 4.25e+01 angle pdb=" C THR A 186 " pdb=" N PRO A 187 " pdb=" CA PRO A 187 " ideal model delta sigma weight residual 121.00 113.85 7.15 1.16e+00 7.43e-01 3.80e+01 ... (remaining 5777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.07: 2317 21.07 - 42.14: 131 42.14 - 63.21: 43 63.21 - 84.28: 4 84.28 - 105.35: 16 Dihedral angle restraints: 2511 sinusoidal: 947 harmonic: 1564 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -157.45 71.45 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS A 599 " pdb=" SG CYS A 599 " pdb=" SG CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sinusoidal sigma weight residual -86.00 -155.91 69.91 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" C TYR A 590 " pdb=" N TYR A 590 " pdb=" CA TYR A 590 " pdb=" CB TYR A 590 " ideal model delta harmonic sigma weight residual -122.60 -139.33 16.73 0 2.50e+00 1.60e-01 4.48e+01 ... (remaining 2508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 672 0.243 - 0.486: 2 0.486 - 0.729: 2 0.729 - 0.972: 1 0.972 - 1.215: 1 Chirality restraints: 678 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.13e+02 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 503 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.69e+01 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 516 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.16e+01 ... (remaining 675 not shown) Planarity restraints: 702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG B 1 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.094 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.310 2.00e-02 2.50e+03 2.61e-01 8.49e+02 pdb=" C7 NAG B 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.448 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " 0.309 2.00e-02 2.50e+03 2.60e-01 8.48e+02 pdb=" C7 NAG A 802 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " -0.448 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " 0.030 2.00e-02 2.50e+03 ... (remaining 699 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1278 2.82 - 3.34: 3822 3.34 - 3.86: 6400 3.86 - 4.38: 7155 4.38 - 4.90: 12360 Nonbonded interactions: 31015 Sorted by model distance: nonbonded pdb=" O SER A 85 " pdb=" OG SER A 89 " model vdw 2.297 3.040 nonbonded pdb=" O GLY A 324 " pdb=" OG SER A 328 " model vdw 2.387 3.040 nonbonded pdb=" O LEU A 507 " pdb=" CD1 LEU A 507 " model vdw 2.400 3.460 nonbonded pdb=" O SER A 491 " pdb=" CD1 PHE A 501 " model vdw 2.463 3.340 nonbonded pdb=" O SER A 371 " pdb=" OG SER A 371 " model vdw 2.475 3.040 ... (remaining 31010 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: 1.200 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: 0.020 Set scattering table: 0.010 Process input model: 5.900 Find NCS groups from input model: 0.010 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 0.316 4268 Z= 0.450 Angle : 1.188 27.121 5805 Z= 0.698 Chirality : 0.086 1.215 678 Planarity : 0.019 0.294 700 Dihedral : 17.751 105.346 1494 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.17 % Allowed : 13.98 % Favored : 83.86 % Cbeta Deviations : 0.20 % 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 aren not related in a simple way. whole: -2.44 (0.31), residues: 539 helix: -0.93 (0.25), residues: 333 sheet: None (None), residues: 0 loop : -2.71 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 526 TYR 0.026 0.002 TYR A 625 PHE 0.012 0.001 PHE A 621 TRP 0.008 0.001 TRP A 171 HIS 0.002 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 4258) covalent geometry : angle 1.00455 ( 5782) SS BOND : bond 0.11957 ( 7) SS BOND : angle 5.91851 ( 14) hydrogen bonds : bond 0.20972 ( 244) hydrogen bonds : angle 6.62794 ( 711) link_BETA1-4 : bond 0.00992 ( 1) link_BETA1-4 : angle 4.76017 ( 3) link_NAG-ASN : bond 0.15759 ( 2) link_NAG-ASN : angle 17.33816 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.162 Fit side-chains REVERT: A 198 ASP cc_start: 0.8666 (m-30) cc_final: 0.8031 (m-30) REVERT: A 253 ARG cc_start: 0.7701 (mtm180) cc_final: 0.6301 (mtp-110) REVERT: A 580 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7566 (mtt90) REVERT: A 623 ARG cc_start: 0.7437 (tpp80) cc_final: 0.7188 (mtm-85) REVERT: A 648 LYS cc_start: 0.7736 (ttmt) cc_final: 0.6993 (ttpt) outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 0.5582 time to fit residues: 48.0405 Evaluate side-chains 59 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 563 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.0050 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.0000 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.156184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116738 restraints weight = 4976.406| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.38 r_work: 0.3181 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4268 Z= 0.153 Angle : 0.762 19.925 5805 Z= 0.353 Chirality : 0.054 0.711 678 Planarity : 0.004 0.050 700 Dihedral : 9.668 54.496 662 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.37 % Allowed : 19.52 % Favored : 77.11 % 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 aren not related in a simple way. whole: -0.35 (0.36), residues: 539 helix: 0.85 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -2.22 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 633 TYR 0.026 0.002 TYR A 590 PHE 0.012 0.001 PHE A 501 TRP 0.005 0.001 TRP A 171 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 4258) covalent geometry : angle 0.65447 ( 5782) SS BOND : bond 0.00738 ( 7) SS BOND : angle 0.82312 ( 14) hydrogen bonds : bond 0.07231 ( 244) hydrogen bonds : angle 4.27108 ( 711) link_BETA1-4 : bond 0.01401 ( 1) link_BETA1-4 : angle 4.52336 ( 3) link_NAG-ASN : bond 0.01560 ( 2) link_NAG-ASN : angle 11.68165 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.162 Fit side-chains REVERT: A 48 MET cc_start: 0.7287 (tpt) cc_final: 0.6978 (tpp) REVERT: A 185 GLU cc_start: 0.8370 (pt0) cc_final: 0.7998 (pp20) REVERT: A 198 ASP cc_start: 0.8398 (m-30) cc_final: 0.7798 (m-30) REVERT: A 253 ARG cc_start: 0.7837 (mtm180) cc_final: 0.6042 (mtp-110) REVERT: A 348 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7576 (tp-100) REVERT: A 623 ARG cc_start: 0.7680 (tpp80) cc_final: 0.7315 (mtt180) REVERT: A 648 LYS cc_start: 0.7568 (ttmt) cc_final: 0.6782 (ttpt) outliers start: 14 outliers final: 4 residues processed: 64 average time/residue: 0.5666 time to fit residues: 37.6582 Evaluate side-chains 54 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111807 restraints weight = 4959.627| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.39 r_work: 0.3146 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4268 Z= 0.157 Angle : 0.702 18.057 5805 Z= 0.334 Chirality : 0.053 0.711 678 Planarity : 0.004 0.049 700 Dihedral : 7.314 58.665 660 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.86 % Allowed : 18.80 % Favored : 77.35 % 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 aren not related in a simple way. whole: 0.34 (0.37), residues: 539 helix: 1.33 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.88 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 633 TYR 0.024 0.002 TYR A 590 PHE 0.014 0.001 PHE A 621 TRP 0.005 0.001 TRP A 470 HIS 0.003 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4258) covalent geometry : angle 0.60606 ( 5782) SS BOND : bond 0.00302 ( 7) SS BOND : angle 0.79279 ( 14) hydrogen bonds : bond 0.07630 ( 244) hydrogen bonds : angle 4.02973 ( 711) link_BETA1-4 : bond 0.00822 ( 1) link_BETA1-4 : angle 3.35991 ( 3) link_NAG-ASN : bond 0.01405 ( 2) link_NAG-ASN : angle 10.75542 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.176 Fit side-chains REVERT: A 48 MET cc_start: 0.7060 (tpt) cc_final: 0.6849 (tpp) REVERT: A 74 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7836 (mm-30) REVERT: A 96 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8219 (mt) REVERT: A 185 GLU cc_start: 0.8426 (pt0) cc_final: 0.7993 (pp20) REVERT: A 251 ASP cc_start: 0.7153 (m-30) cc_final: 0.6550 (m-30) REVERT: A 253 ARG cc_start: 0.7874 (mtm180) cc_final: 0.6047 (mtp-110) REVERT: A 348 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7702 (tp-100) REVERT: A 623 ARG cc_start: 0.7766 (tpp80) cc_final: 0.7458 (mtm-85) REVERT: A 648 LYS cc_start: 0.7602 (ttmt) cc_final: 0.6858 (ttpt) outliers start: 16 outliers final: 7 residues processed: 59 average time/residue: 0.5291 time to fit residues: 32.4918 Evaluate side-chains 59 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.149934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111976 restraints weight = 4949.416| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.16 r_work: 0.3166 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4268 Z= 0.142 Angle : 0.654 16.592 5805 Z= 0.312 Chirality : 0.050 0.653 678 Planarity : 0.004 0.049 700 Dihedral : 6.708 54.538 660 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.86 % Allowed : 19.76 % Favored : 76.39 % 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 aren not related in a simple way. whole: 0.84 (0.37), residues: 539 helix: 1.68 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.58 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 633 TYR 0.024 0.001 TYR A 590 PHE 0.014 0.001 PHE A 501 TRP 0.005 0.001 TRP A 171 HIS 0.002 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4258) covalent geometry : angle 0.56705 ( 5782) SS BOND : bond 0.00262 ( 7) SS BOND : angle 0.62725 ( 14) hydrogen bonds : bond 0.06979 ( 244) hydrogen bonds : angle 3.85820 ( 711) link_BETA1-4 : bond 0.00697 ( 1) link_BETA1-4 : angle 3.15240 ( 3) link_NAG-ASN : bond 0.01353 ( 2) link_NAG-ASN : angle 9.87981 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.158 Fit side-chains REVERT: A 185 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7947 (pp20) REVERT: A 198 ASP cc_start: 0.8179 (m-30) cc_final: 0.7533 (m-30) REVERT: A 253 ARG cc_start: 0.7823 (mtm180) cc_final: 0.6021 (mtp-110) REVERT: A 348 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7222 (tp-100) REVERT: A 623 ARG cc_start: 0.7361 (tpp80) cc_final: 0.7056 (mtm-85) REVERT: A 648 LYS cc_start: 0.7220 (ttmt) cc_final: 0.6479 (ttpt) outliers start: 16 outliers final: 7 residues processed: 64 average time/residue: 0.4756 time to fit residues: 31.8282 Evaluate side-chains 57 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 636 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.150641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112076 restraints weight = 5023.439| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.33 r_work: 0.3152 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4268 Z= 0.145 Angle : 0.648 16.063 5805 Z= 0.309 Chirality : 0.049 0.641 678 Planarity : 0.004 0.048 700 Dihedral : 6.695 55.072 660 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.86 % Allowed : 20.24 % Favored : 75.90 % 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 aren not related in a simple way. whole: 1.07 (0.38), residues: 539 helix: 1.84 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.44 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 633 TYR 0.023 0.001 TYR A 625 PHE 0.014 0.001 PHE A 621 TRP 0.004 0.001 TRP A 171 HIS 0.002 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4258) covalent geometry : angle 0.56763 ( 5782) SS BOND : bond 0.00274 ( 7) SS BOND : angle 0.54267 ( 14) hydrogen bonds : bond 0.07172 ( 244) hydrogen bonds : angle 3.81338 ( 711) link_BETA1-4 : bond 0.00584 ( 1) link_BETA1-4 : angle 2.91699 ( 3) link_NAG-ASN : bond 0.01357 ( 2) link_NAG-ASN : angle 9.55366 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.111 Fit side-chains REVERT: A 185 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7989 (pp20) REVERT: A 198 ASP cc_start: 0.8181 (m-30) cc_final: 0.7572 (m-30) REVERT: A 253 ARG cc_start: 0.7806 (mtm180) cc_final: 0.5957 (mtp-110) REVERT: A 348 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7231 (tp-100) REVERT: A 563 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7908 (p) REVERT: A 623 ARG cc_start: 0.7385 (tpp80) cc_final: 0.6989 (mtt180) REVERT: A 648 LYS cc_start: 0.7118 (ttmt) cc_final: 0.6416 (ttpt) outliers start: 16 outliers final: 8 residues processed: 58 average time/residue: 0.5436 time to fit residues: 32.7890 Evaluate side-chains 57 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 647 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.152204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113509 restraints weight = 5077.258| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.37 r_work: 0.3126 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4268 Z= 0.140 Angle : 0.649 15.919 5805 Z= 0.312 Chirality : 0.049 0.630 678 Planarity : 0.004 0.048 700 Dihedral : 6.774 54.666 660 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.61 % Allowed : 20.24 % Favored : 76.14 % 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 aren not related in a simple way. whole: 1.16 (0.38), residues: 539 helix: 2.05 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.60 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 633 TYR 0.023 0.001 TYR A 590 PHE 0.016 0.001 PHE A 386 TRP 0.004 0.001 TRP A 258 HIS 0.002 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4258) covalent geometry : angle 0.56665 ( 5782) SS BOND : bond 0.00237 ( 7) SS BOND : angle 1.41655 ( 14) hydrogen bonds : bond 0.06907 ( 244) hydrogen bonds : angle 3.77066 ( 711) link_BETA1-4 : bond 0.00649 ( 1) link_BETA1-4 : angle 2.90585 ( 3) link_NAG-ASN : bond 0.01384 ( 2) link_NAG-ASN : angle 9.43862 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.191 Fit side-chains REVERT: A 185 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8018 (pp20) REVERT: A 198 ASP cc_start: 0.8167 (m-30) cc_final: 0.7537 (m-30) REVERT: A 253 ARG cc_start: 0.7789 (mtm180) cc_final: 0.5947 (mtp-110) REVERT: A 348 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.7216 (tp-100) REVERT: A 563 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7892 (p) REVERT: A 623 ARG cc_start: 0.7283 (tpp80) cc_final: 0.6904 (mtt180) REVERT: A 648 LYS cc_start: 0.6957 (ttmt) cc_final: 0.6264 (ttpt) outliers start: 15 outliers final: 8 residues processed: 58 average time/residue: 0.5222 time to fit residues: 31.5521 Evaluate side-chains 58 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 647 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.150035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110980 restraints weight = 5060.224| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.38 r_work: 0.3134 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4268 Z= 0.149 Angle : 0.648 15.569 5805 Z= 0.312 Chirality : 0.049 0.613 678 Planarity : 0.004 0.046 700 Dihedral : 6.779 56.224 660 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.86 % Allowed : 20.72 % Favored : 75.42 % 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 aren not related in a simple way. whole: 1.21 (0.37), residues: 539 helix: 2.09 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.57 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 623 TYR 0.023 0.002 TYR A 625 PHE 0.015 0.001 PHE A 621 TRP 0.004 0.001 TRP A 254 HIS 0.002 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4258) covalent geometry : angle 0.57131 ( 5782) SS BOND : bond 0.00250 ( 7) SS BOND : angle 1.28353 ( 14) hydrogen bonds : bond 0.07365 ( 244) hydrogen bonds : angle 3.84357 ( 711) link_BETA1-4 : bond 0.00486 ( 1) link_BETA1-4 : angle 2.65263 ( 3) link_NAG-ASN : bond 0.01404 ( 2) link_NAG-ASN : angle 9.20759 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.180 Fit side-chains REVERT: A 198 ASP cc_start: 0.8620 (m-30) cc_final: 0.7994 (m-30) REVERT: A 247 ILE cc_start: 0.8678 (pt) cc_final: 0.8336 (tp) REVERT: A 348 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7804 (tp-100) REVERT: A 440 MET cc_start: 0.8223 (ptm) cc_final: 0.7958 (ptt) REVERT: A 563 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8215 (p) REVERT: A 623 ARG cc_start: 0.7786 (tpp80) cc_final: 0.7380 (mtt180) REVERT: A 648 LYS cc_start: 0.7503 (ttmt) cc_final: 0.6794 (ttpt) outliers start: 16 outliers final: 8 residues processed: 62 average time/residue: 0.4841 time to fit residues: 31.3449 Evaluate side-chains 58 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 647 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 0.0050 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.0050 chunk 10 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 0.0770 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.2966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.157964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119078 restraints weight = 5012.723| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.50 r_work: 0.3224 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4268 Z= 0.119 Angle : 0.615 15.433 5805 Z= 0.292 Chirality : 0.048 0.612 678 Planarity : 0.004 0.049 700 Dihedral : 6.523 54.194 660 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.13 % Allowed : 22.65 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.38), residues: 539 helix: 2.37 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.48 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 181 TYR 0.024 0.001 TYR A 590 PHE 0.014 0.001 PHE A 386 TRP 0.004 0.001 TRP A 171 HIS 0.001 0.000 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 4258) covalent geometry : angle 0.53857 ( 5782) SS BOND : bond 0.00164 ( 7) SS BOND : angle 0.81322 ( 14) hydrogen bonds : bond 0.05210 ( 244) hydrogen bonds : angle 3.56955 ( 711) link_BETA1-4 : bond 0.00712 ( 1) link_BETA1-4 : angle 2.91410 ( 3) link_NAG-ASN : bond 0.01476 ( 2) link_NAG-ASN : angle 9.00072 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.164 Fit side-chains REVERT: A 198 ASP cc_start: 0.8416 (m-30) cc_final: 0.7803 (m-30) REVERT: A 247 ILE cc_start: 0.8645 (pt) cc_final: 0.8389 (tp) REVERT: A 253 ARG cc_start: 0.7921 (mtm180) cc_final: 0.6003 (mmm160) REVERT: A 348 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7485 (tp-100) REVERT: A 417 MET cc_start: 0.8746 (tpp) cc_final: 0.8481 (mmm) REVERT: A 440 MET cc_start: 0.8126 (ptm) cc_final: 0.7906 (ptt) REVERT: A 563 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7994 (p) outliers start: 13 outliers final: 5 residues processed: 57 average time/residue: 0.4745 time to fit residues: 28.2793 Evaluate side-chains 55 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 563 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.0040 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.0050 chunk 47 optimal weight: 0.9980 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114406 restraints weight = 5115.207| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.43 r_work: 0.3176 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4268 Z= 0.129 Angle : 0.630 15.345 5805 Z= 0.299 Chirality : 0.048 0.606 678 Planarity : 0.004 0.048 700 Dihedral : 6.188 53.779 659 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.17 % Allowed : 23.86 % Favored : 73.98 % 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 aren not related in a simple way. whole: 1.53 (0.38), residues: 539 helix: 2.24 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.34 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 623 TYR 0.023 0.001 TYR A 590 PHE 0.016 0.001 PHE A 386 TRP 0.003 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4258) covalent geometry : angle 0.55724 ( 5782) SS BOND : bond 0.00207 ( 7) SS BOND : angle 0.85703 ( 14) hydrogen bonds : bond 0.06131 ( 244) hydrogen bonds : angle 3.62470 ( 711) link_BETA1-4 : bond 0.00425 ( 1) link_BETA1-4 : angle 2.62344 ( 3) link_NAG-ASN : bond 0.01442 ( 2) link_NAG-ASN : angle 8.90947 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.165 Fit side-chains REVERT: A 198 ASP cc_start: 0.8576 (m-30) cc_final: 0.7960 (m-30) REVERT: A 247 ILE cc_start: 0.8664 (pt) cc_final: 0.8399 (tp) REVERT: A 253 ARG cc_start: 0.7963 (mtm180) cc_final: 0.6069 (mmm160) REVERT: A 348 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7670 (tp-100) REVERT: A 417 MET cc_start: 0.8834 (tpp) cc_final: 0.8569 (mmm) REVERT: A 440 MET cc_start: 0.8234 (ptm) cc_final: 0.7999 (ptt) REVERT: A 563 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.8004 (p) REVERT: A 605 ASN cc_start: 0.6587 (t0) cc_final: 0.5823 (p0) outliers start: 9 outliers final: 7 residues processed: 53 average time/residue: 0.4946 time to fit residues: 27.3921 Evaluate side-chains 55 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 563 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.149551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110165 restraints weight = 5024.772| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.37 r_work: 0.3125 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4268 Z= 0.158 Angle : 0.652 15.388 5805 Z= 0.315 Chirality : 0.049 0.611 678 Planarity : 0.004 0.046 700 Dihedral : 6.264 54.171 659 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.41 % Allowed : 23.61 % Favored : 73.98 % 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 aren not related in a simple way. whole: 1.41 (0.38), residues: 539 helix: 2.13 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.35 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 623 TYR 0.023 0.002 TYR A 625 PHE 0.016 0.001 PHE A 386 TRP 0.004 0.001 TRP A 254 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4258) covalent geometry : angle 0.58318 ( 5782) SS BOND : bond 0.00264 ( 7) SS BOND : angle 0.95149 ( 14) hydrogen bonds : bond 0.07444 ( 244) hydrogen bonds : angle 3.80493 ( 711) link_BETA1-4 : bond 0.00439 ( 1) link_BETA1-4 : angle 2.32938 ( 3) link_NAG-ASN : bond 0.01396 ( 2) link_NAG-ASN : angle 8.89245 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.165 Fit side-chains REVERT: A 198 ASP cc_start: 0.8577 (m-30) cc_final: 0.7930 (m-30) REVERT: A 247 ILE cc_start: 0.8721 (pt) cc_final: 0.8402 (tp) REVERT: A 348 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7789 (tp-100) REVERT: A 417 MET cc_start: 0.8867 (tpp) cc_final: 0.8571 (mmm) REVERT: A 563 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8133 (p) REVERT: A 623 ARG cc_start: 0.7768 (tpp80) cc_final: 0.7401 (mtt180) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.5337 time to fit residues: 30.0288 Evaluate side-chains 55 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 563 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117194 restraints weight = 5055.272| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.41 r_work: 0.3217 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4268 Z= 0.119 Angle : 0.611 15.349 5805 Z= 0.291 Chirality : 0.048 0.604 678 Planarity : 0.004 0.050 700 Dihedral : 6.078 53.543 659 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.69 % Allowed : 24.34 % Favored : 73.98 % 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 aren not related in a simple way. whole: 1.65 (0.38), residues: 539 helix: 2.33 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.30 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 181 TYR 0.024 0.001 TYR A 590 PHE 0.017 0.001 PHE A 386 TRP 0.005 0.001 TRP A 171 HIS 0.001 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 4258) covalent geometry : angle 0.53914 ( 5782) SS BOND : bond 0.00200 ( 7) SS BOND : angle 0.61010 ( 14) hydrogen bonds : bond 0.05368 ( 244) hydrogen bonds : angle 3.57054 ( 711) link_BETA1-4 : bond 0.00308 ( 1) link_BETA1-4 : angle 2.65424 ( 3) link_NAG-ASN : bond 0.01466 ( 2) link_NAG-ASN : angle 8.73509 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1713.02 seconds wall clock time: 30 minutes 8.11 seconds (1808.11 seconds total)