Starting phenix.real_space_refine on Fri Aug 22 14:55:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnc_34910/08_2025/8hnc_34910.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnc_34910/08_2025/8hnc_34910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hnc_34910/08_2025/8hnc_34910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnc_34910/08_2025/8hnc_34910.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hnc_34910/08_2025/8hnc_34910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnc_34910/08_2025/8hnc_34910.map" } resolution = 3.73 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= 0.041 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 2825 2.51 5 N 678 2.21 5 O 736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s 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: 4272 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4187 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 21, 'TRANS': 548} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 4, 'TYR:plan': 5, 'ASP:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 10} Unresolved non-hydrogen planarities: 132 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: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'BLR': 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: 1.28, per 1000 atoms: 0.30 Number of scatterers: 4272 At special positions: 0 Unit cell: (101.504, 59.904, 79.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 736 8.00 N 678 7.00 C 2825 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=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.01 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 704 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 170.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 1 sheets defined 66.1% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 26 through 49 removed outlier: 4.087A pdb=" N PHE A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 58 Processing helix chain 'A' and resid 62 through 79 removed outlier: 4.505A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.946A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (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 113 Processing helix chain 'A' and resid 114 through 117 Processing helix chain 'A' and resid 121 through 125 removed outlier: 4.652A pdb=" N LYS A 125 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.085A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 removed outlier: 3.844A pdb=" N SER A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 217 through 231 Processing helix chain 'A' and resid 258 through 274 removed outlier: 3.594A pdb=" N PHE A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.815A pdb=" N LEU A 279 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 335 through 366 removed outlier: 5.253A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 400 removed outlier: 3.757A pdb=" N GLY A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 403 through 426 removed outlier: 3.767A pdb=" N PHE A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 550 removed outlier: 3.827A pdb=" N LYS A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 removed outlier: 3.537A pdb=" N VAL A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 567 through 584 Processing helix chain 'A' and resid 586 through 597 Processing helix chain 'A' and resid 617 through 651 Processing sheet with id=AA1, first strand: chain 'A' and resid 480 through 481 263 hydrogen bonds defined for protein. 777 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: 0.43 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: 1.20 - 1.32: 664 1.32 - 1.45: 1233 1.45 - 1.57: 2432 1.57 - 1.69: 0 1.69 - 1.82: 49 Bond restraints: 4378 Sorted by residual: bond pdb=" CGD BLR A 701 " pdb=" O1D BLR A 701 " ideal model delta sigma weight residual 1.231 1.308 -0.077 2.00e-02 2.50e+03 1.46e+01 bond pdb=" N LEU A 545 " pdb=" CA LEU A 545 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.28e-02 6.10e+03 1.31e+01 bond pdb=" C TYR A 352 " pdb=" O TYR A 352 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" CA LEU A 545 " pdb=" C LEU A 545 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.35e-02 5.49e+03 9.96e+00 bond pdb=" CA TYR A 352 " pdb=" C TYR A 352 " ideal model delta sigma weight residual 1.524 1.483 0.041 1.32e-02 5.74e+03 9.53e+00 ... (remaining 4373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 5701 2.22 - 4.44: 206 4.44 - 6.66: 32 6.66 - 8.88: 9 8.88 - 11.10: 3 Bond angle restraints: 5951 Sorted by residual: angle pdb=" N VAL A 509 " pdb=" CA VAL A 509 " pdb=" C VAL A 509 " ideal model delta sigma weight residual 110.62 118.68 -8.06 1.02e+00 9.61e-01 6.25e+01 angle pdb=" N ASN A 503 " pdb=" CA ASN A 503 " pdb=" C ASN A 503 " ideal model delta sigma weight residual 111.56 122.66 -11.10 1.43e+00 4.89e-01 6.02e+01 angle pdb=" C THR A 186 " pdb=" N PRO A 187 " pdb=" CA PRO A 187 " ideal model delta sigma weight residual 121.65 115.05 6.60 1.01e+00 9.80e-01 4.27e+01 angle pdb=" C TRP A 254 " pdb=" N VAL A 255 " pdb=" CA VAL A 255 " ideal model delta sigma weight residual 122.99 114.19 8.80 1.39e+00 5.18e-01 4.01e+01 angle pdb=" C THR A 510 " pdb=" N GLY A 511 " pdb=" CA GLY A 511 " ideal model delta sigma weight residual 121.58 116.85 4.73 8.60e-01 1.35e+00 3.02e+01 ... (remaining 5946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.20: 2389 21.20 - 42.40: 142 42.40 - 63.60: 13 63.60 - 84.79: 11 84.79 - 105.99: 8 Dihedral angle restraints: 2563 sinusoidal: 936 harmonic: 1627 Sorted by residual: dihedral pdb=" CB CYS A 459 " pdb=" SG CYS A 459 " pdb=" SG CYS A 506 " pdb=" CB CYS A 506 " ideal model delta sinusoidal sigma weight residual 93.00 175.59 -82.59 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 463 " pdb=" CB CYS A 463 " ideal model delta sinusoidal sigma weight residual 93.00 14.62 78.38 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" C LEU A 143 " pdb=" N LEU A 143 " pdb=" CA LEU A 143 " pdb=" CB LEU A 143 " ideal model delta harmonic sigma weight residual -122.60 -110.31 -12.29 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 2560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 691 0.294 - 0.587: 3 0.587 - 0.881: 0 0.881 - 1.175: 0 1.175 - 1.468: 1 Chirality restraints: 695 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 -0.93 -1.47 2.00e-02 2.50e+03 5.39e+03 chirality pdb=" CA ASN A 503 " pdb=" N ASN A 503 " pdb=" C ASN A 503 " pdb=" CB ASN A 503 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA ASN A 460 " pdb=" N ASN A 460 " pdb=" C ASN A 460 " pdb=" CB ASN A 460 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 692 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.313 2.00e-02 2.50e+03 2.66e-01 8.82e+02 pdb=" C7 NAG B 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.463 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.286 2.00e-02 2.50e+03 2.44e-01 7.46e+02 pdb=" C7 NAG B 1 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.018 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.412 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " -0.159 2.00e-02 2.50e+03 1.31e-01 2.14e+02 pdb=" C7 NAG A 704 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " -0.118 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " 0.210 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " 0.022 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 53 2.64 - 3.21: 4287 3.21 - 3.77: 6608 3.77 - 4.34: 8538 4.34 - 4.90: 13867 Nonbonded interactions: 33353 Sorted by model distance: nonbonded pdb=" ND BLR A 701 " pdb=" O2A BLR A 701 " model vdw 2.079 3.120 nonbonded pdb=" O MET A 233 " pdb=" N ALA A 257 " model vdw 2.204 3.120 nonbonded pdb=" O ASN A 460 " pdb=" N CYS A 463 " model vdw 2.224 3.120 nonbonded pdb=" OG SER A 418 " pdb=" ND2 ASN A 544 " model vdw 2.293 3.120 nonbonded pdb=" ND1 HIS A 115 " pdb=" CD1 TRP A 259 " model vdw 2.364 3.340 ... (remaining 33348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.690 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 0.382 4388 Z= 0.463 Angle : 1.277 52.004 5974 Z= 0.691 Chirality : 0.081 1.468 695 Planarity : 0.015 0.266 726 Dihedral : 15.074 105.991 1506 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.49 % Allowed : 5.11 % Favored : 94.40 % Cbeta Deviations : 0.39 % 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: -2.79 (0.31), residues: 562 helix: -1.27 (0.24), residues: 343 sheet: None (None), residues: 0 loop : -2.72 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 57 TYR 0.025 0.002 TYR A 352 PHE 0.029 0.001 PHE A 591 TRP 0.006 0.001 TRP A 258 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00616 ( 4378) covalent geometry : angle 1.00940 ( 5951) SS BOND : bond 0.00877 ( 7) SS BOND : angle 1.36399 ( 14) hydrogen bonds : bond 0.15315 ( 263) hydrogen bonds : angle 7.41183 ( 777) link_BETA1-4 : bond 0.38155 ( 1) link_BETA1-4 : angle 31.45835 ( 3) link_NAG-ASN : bond 0.00145 ( 2) link_NAG-ASN : angle 10.72764 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8898 (tpt) cc_final: 0.8483 (tpp) REVERT: A 185 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 381 ILE cc_start: 0.8682 (tp) cc_final: 0.8426 (tp) REVERT: A 617 ASN cc_start: 0.7996 (t0) cc_final: 0.7607 (t0) outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 0.0793 time to fit residues: 10.2862 Evaluate side-chains 76 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.168384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.117940 restraints weight = 4842.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.119943 restraints weight = 3789.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.121123 restraints weight = 3221.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.122184 restraints weight = 2911.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.122452 restraints weight = 2730.648| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4388 Z= 0.157 Angle : 0.694 13.068 5974 Z= 0.327 Chirality : 0.044 0.277 695 Planarity : 0.004 0.039 726 Dihedral : 8.754 85.996 680 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.46 % Allowed : 14.60 % Favored : 83.94 % 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: -0.49 (0.34), residues: 562 helix: 0.57 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -1.79 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 526 TYR 0.028 0.002 TYR A 590 PHE 0.013 0.001 PHE A 591 TRP 0.006 0.001 TRP A 470 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4378) covalent geometry : angle 0.65749 ( 5951) SS BOND : bond 0.00182 ( 7) SS BOND : angle 1.06508 ( 14) hydrogen bonds : bond 0.04706 ( 263) hydrogen bonds : angle 4.80548 ( 777) link_BETA1-4 : bond 0.01360 ( 1) link_BETA1-4 : angle 8.42454 ( 3) link_NAG-ASN : bond 0.00236 ( 2) link_NAG-ASN : angle 3.63747 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8950 (tpt) cc_final: 0.8518 (tpp) REVERT: A 254 TRP cc_start: 0.7932 (t-100) cc_final: 0.7706 (t-100) REVERT: A 381 ILE cc_start: 0.8740 (tp) cc_final: 0.8427 (tp) REVERT: A 390 MET cc_start: 0.8380 (mmt) cc_final: 0.7802 (mmt) outliers start: 6 outliers final: 3 residues processed: 85 average time/residue: 0.0664 time to fit residues: 7.3866 Evaluate side-chains 80 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** 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 = 0.3976 r_free = 0.3976 target = 0.184994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.128077 restraints weight = 4987.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.131717 restraints weight = 3271.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.133981 restraints weight = 2544.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.135094 restraints weight = 2182.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.136404 restraints weight = 2009.859| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4388 Z= 0.143 Angle : 0.624 11.102 5974 Z= 0.296 Chirality : 0.042 0.277 695 Planarity : 0.004 0.040 726 Dihedral : 7.436 83.182 680 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.68 % Allowed : 17.03 % 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 aren not related in a simple way. whole: 0.36 (0.36), residues: 562 helix: 1.27 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -1.42 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 526 TYR 0.024 0.002 TYR A 590 PHE 0.013 0.001 PHE A 591 TRP 0.006 0.001 TRP A 254 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4378) covalent geometry : angle 0.59177 ( 5951) SS BOND : bond 0.00118 ( 7) SS BOND : angle 0.70799 ( 14) hydrogen bonds : bond 0.04336 ( 263) hydrogen bonds : angle 4.44454 ( 777) link_BETA1-4 : bond 0.00540 ( 1) link_BETA1-4 : angle 7.05150 ( 3) link_NAG-ASN : bond 0.00180 ( 2) link_NAG-ASN : angle 3.85795 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8810 (tpt) cc_final: 0.8394 (tpp) REVERT: A 170 MET cc_start: 0.7981 (mmm) cc_final: 0.7666 (mmm) REVERT: A 198 ASP cc_start: 0.8745 (t0) cc_final: 0.8544 (t0) REVERT: A 254 TRP cc_start: 0.8077 (t-100) cc_final: 0.7803 (t-100) REVERT: A 381 ILE cc_start: 0.8562 (tp) cc_final: 0.8268 (tp) REVERT: A 390 MET cc_start: 0.8183 (mmt) cc_final: 0.7528 (mmt) outliers start: 11 outliers final: 6 residues processed: 87 average time/residue: 0.0587 time to fit residues: 6.8467 Evaluate side-chains 82 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.208939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.156473 restraints weight = 4909.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.160229 restraints weight = 3184.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.162373 restraints weight = 2435.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.164225 restraints weight = 2089.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.164920 restraints weight = 1892.192| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4388 Z= 0.140 Angle : 0.603 9.646 5974 Z= 0.291 Chirality : 0.041 0.208 695 Planarity : 0.004 0.040 726 Dihedral : 7.124 80.302 680 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.92 % Allowed : 18.00 % Favored : 79.08 % 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: 0.61 (0.36), residues: 562 helix: 1.47 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.38 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 526 TYR 0.024 0.002 TYR A 590 PHE 0.012 0.001 PHE A 591 TRP 0.007 0.001 TRP A 254 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4378) covalent geometry : angle 0.57643 ( 5951) SS BOND : bond 0.00143 ( 7) SS BOND : angle 0.75888 ( 14) hydrogen bonds : bond 0.04186 ( 263) hydrogen bonds : angle 4.27332 ( 777) link_BETA1-4 : bond 0.00793 ( 1) link_BETA1-4 : angle 6.16492 ( 3) link_NAG-ASN : bond 0.00218 ( 2) link_NAG-ASN : angle 3.45924 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8953 (tpt) cc_final: 0.8547 (tpp) REVERT: A 170 MET cc_start: 0.7807 (mmm) cc_final: 0.7508 (mmm) REVERT: A 381 ILE cc_start: 0.8776 (tp) cc_final: 0.8474 (tp) REVERT: A 390 MET cc_start: 0.8252 (mmt) cc_final: 0.7631 (mmt) outliers start: 12 outliers final: 6 residues processed: 87 average time/residue: 0.0576 time to fit residues: 6.8399 Evaluate side-chains 85 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 51 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.215008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.164696 restraints weight = 4812.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.168683 restraints weight = 2905.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.170932 restraints weight = 2134.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.172616 restraints weight = 1786.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.173370 restraints weight = 1602.505| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4388 Z= 0.136 Angle : 0.599 9.070 5974 Z= 0.290 Chirality : 0.041 0.216 695 Planarity : 0.003 0.040 726 Dihedral : 6.942 78.191 680 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.14 % Allowed : 18.25 % Favored : 77.62 % 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: 0.81 (0.36), residues: 562 helix: 1.56 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -1.20 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 526 TYR 0.023 0.001 TYR A 590 PHE 0.010 0.001 PHE A 591 TRP 0.004 0.001 TRP A 470 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4378) covalent geometry : angle 0.57309 ( 5951) SS BOND : bond 0.00096 ( 7) SS BOND : angle 1.36284 ( 14) hydrogen bonds : bond 0.04075 ( 263) hydrogen bonds : angle 4.18074 ( 777) link_BETA1-4 : bond 0.00605 ( 1) link_BETA1-4 : angle 5.73759 ( 3) link_NAG-ASN : bond 0.00193 ( 2) link_NAG-ASN : angle 3.22773 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8848 (tpt) cc_final: 0.8462 (tpp) REVERT: A 176 MET cc_start: 0.8120 (tpp) cc_final: 0.7861 (mmt) REVERT: A 381 ILE cc_start: 0.8701 (tp) cc_final: 0.8383 (tp) REVERT: A 390 MET cc_start: 0.8170 (mmt) cc_final: 0.7438 (mmt) outliers start: 17 outliers final: 8 residues processed: 89 average time/residue: 0.0577 time to fit residues: 6.9437 Evaluate side-chains 86 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 45 optimal weight: 0.0980 chunk 38 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.216261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.166836 restraints weight = 4835.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.170553 restraints weight = 3054.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.172644 restraints weight = 2296.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.174266 restraints weight = 1944.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.174873 restraints weight = 1754.734| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4388 Z= 0.127 Angle : 0.608 9.942 5974 Z= 0.288 Chirality : 0.041 0.195 695 Planarity : 0.003 0.039 726 Dihedral : 6.775 74.984 680 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.14 % Allowed : 19.22 % Favored : 76.64 % 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: 1.01 (0.37), residues: 562 helix: 1.73 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -1.15 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 526 TYR 0.023 0.002 TYR A 590 PHE 0.010 0.001 PHE A 591 TRP 0.004 0.001 TRP A 470 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4378) covalent geometry : angle 0.58461 ( 5951) SS BOND : bond 0.00140 ( 7) SS BOND : angle 1.68158 ( 14) hydrogen bonds : bond 0.03929 ( 263) hydrogen bonds : angle 4.09246 ( 777) link_BETA1-4 : bond 0.00539 ( 1) link_BETA1-4 : angle 5.30065 ( 3) link_NAG-ASN : bond 0.00252 ( 2) link_NAG-ASN : angle 2.88755 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8886 (tpt) cc_final: 0.8521 (tpp) REVERT: A 170 MET cc_start: 0.7498 (mmm) cc_final: 0.7220 (mmm) REVERT: A 381 ILE cc_start: 0.8741 (tp) cc_final: 0.8433 (tp) REVERT: A 390 MET cc_start: 0.8169 (mmt) cc_final: 0.7438 (mmt) outliers start: 17 outliers final: 12 residues processed: 89 average time/residue: 0.0563 time to fit residues: 6.7599 Evaluate side-chains 87 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.165619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.119140 restraints weight = 4915.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.116015 restraints weight = 4502.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.118274 restraints weight = 4158.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.119011 restraints weight = 3332.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.119251 restraints weight = 2909.369| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4388 Z= 0.139 Angle : 0.622 8.184 5974 Z= 0.297 Chirality : 0.041 0.194 695 Planarity : 0.003 0.040 726 Dihedral : 6.653 74.672 680 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.65 % Allowed : 20.44 % Favored : 75.91 % 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 aren not related in a simple way. whole: 1.06 (0.37), residues: 562 helix: 1.80 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -1.18 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 526 TYR 0.023 0.002 TYR A 590 PHE 0.010 0.001 PHE A 591 TRP 0.004 0.001 TRP A 171 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4378) covalent geometry : angle 0.59851 ( 5951) SS BOND : bond 0.00232 ( 7) SS BOND : angle 2.06014 ( 14) hydrogen bonds : bond 0.03970 ( 263) hydrogen bonds : angle 4.09614 ( 777) link_BETA1-4 : bond 0.00488 ( 1) link_BETA1-4 : angle 4.99810 ( 3) link_NAG-ASN : bond 0.00243 ( 2) link_NAG-ASN : angle 2.70022 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8786 (tpt) cc_final: 0.8414 (tpp) REVERT: A 254 TRP cc_start: 0.7692 (t-100) cc_final: 0.7270 (t60) REVERT: A 381 ILE cc_start: 0.8598 (tp) cc_final: 0.8274 (tp) outliers start: 15 outliers final: 12 residues processed: 83 average time/residue: 0.0590 time to fit residues: 6.5784 Evaluate side-chains 85 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 37 optimal weight: 0.0670 chunk 40 optimal weight: 0.0980 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 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 = 0.3766 r_free = 0.3766 target = 0.168398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.122146 restraints weight = 4843.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.119523 restraints weight = 4486.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.120182 restraints weight = 4486.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.120878 restraints weight = 3791.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.121180 restraints weight = 3402.989| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4388 Z= 0.118 Angle : 0.584 8.240 5974 Z= 0.280 Chirality : 0.040 0.191 695 Planarity : 0.004 0.039 726 Dihedral : 6.416 70.241 680 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.65 % Allowed : 19.95 % Favored : 76.40 % 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: 1.20 (0.37), residues: 562 helix: 1.89 (0.29), residues: 349 sheet: None (None), residues: 0 loop : -1.11 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 526 TYR 0.024 0.001 TYR A 590 PHE 0.015 0.001 PHE A 116 TRP 0.004 0.001 TRP A 171 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4378) covalent geometry : angle 0.56538 ( 5951) SS BOND : bond 0.00170 ( 7) SS BOND : angle 1.52833 ( 14) hydrogen bonds : bond 0.03705 ( 263) hydrogen bonds : angle 3.97478 ( 777) link_BETA1-4 : bond 0.00590 ( 1) link_BETA1-4 : angle 4.65149 ( 3) link_NAG-ASN : bond 0.00279 ( 2) link_NAG-ASN : angle 2.56656 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8701 (tpt) cc_final: 0.8383 (tpp) REVERT: A 220 PRO cc_start: 0.8949 (Cg_exo) cc_final: 0.8734 (Cg_endo) REVERT: A 254 TRP cc_start: 0.7774 (t-100) cc_final: 0.7328 (t60) REVERT: A 381 ILE cc_start: 0.8536 (tp) cc_final: 0.8211 (tp) outliers start: 15 outliers final: 12 residues processed: 85 average time/residue: 0.0601 time to fit residues: 6.8743 Evaluate side-chains 83 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 19 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** 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 = 0.3755 r_free = 0.3755 target = 0.167372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.120845 restraints weight = 4861.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.118334 restraints weight = 4468.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.119390 restraints weight = 3957.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.120145 restraints weight = 3582.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.120403 restraints weight = 3165.606| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4388 Z= 0.123 Angle : 0.585 7.735 5974 Z= 0.280 Chirality : 0.041 0.192 695 Planarity : 0.003 0.040 726 Dihedral : 6.313 70.292 680 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.41 % Allowed : 21.90 % Favored : 74.70 % 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: 1.25 (0.37), residues: 562 helix: 1.91 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -1.04 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 526 TYR 0.023 0.001 TYR A 590 PHE 0.013 0.001 PHE A 427 TRP 0.003 0.001 TRP A 171 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4378) covalent geometry : angle 0.56732 ( 5951) SS BOND : bond 0.00084 ( 7) SS BOND : angle 1.52351 ( 14) hydrogen bonds : bond 0.03783 ( 263) hydrogen bonds : angle 4.00756 ( 777) link_BETA1-4 : bond 0.00590 ( 1) link_BETA1-4 : angle 4.44082 ( 3) link_NAG-ASN : bond 0.00263 ( 2) link_NAG-ASN : angle 2.48299 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8695 (tpt) cc_final: 0.8349 (tpp) REVERT: A 176 MET cc_start: 0.7922 (tpp) cc_final: 0.7434 (tpp) REVERT: A 254 TRP cc_start: 0.7830 (t-100) cc_final: 0.7347 (t60) REVERT: A 356 PHE cc_start: 0.7237 (m-80) cc_final: 0.6693 (t80) REVERT: A 381 ILE cc_start: 0.8576 (tp) cc_final: 0.8250 (tp) outliers start: 14 outliers final: 13 residues processed: 83 average time/residue: 0.0588 time to fit residues: 6.5875 Evaluate side-chains 86 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.0270 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** 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 = 0.3753 r_free = 0.3753 target = 0.167092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.121289 restraints weight = 4884.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.118278 restraints weight = 4636.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.119076 restraints weight = 4430.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.119696 restraints weight = 3829.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.119920 restraints weight = 3432.037| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4388 Z= 0.127 Angle : 0.604 7.663 5974 Z= 0.289 Chirality : 0.042 0.290 695 Planarity : 0.003 0.033 726 Dihedral : 6.285 70.505 680 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.92 % Allowed : 22.38 % Favored : 74.70 % 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: 1.26 (0.37), residues: 562 helix: 1.91 (0.29), residues: 349 sheet: None (None), residues: 0 loop : -1.03 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 526 TYR 0.023 0.001 TYR A 590 PHE 0.011 0.001 PHE A 427 TRP 0.003 0.000 TRP A 171 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 4378) covalent geometry : angle 0.58776 ( 5951) SS BOND : bond 0.00078 ( 7) SS BOND : angle 1.42614 ( 14) hydrogen bonds : bond 0.03828 ( 263) hydrogen bonds : angle 4.00607 ( 777) link_BETA1-4 : bond 0.00657 ( 1) link_BETA1-4 : angle 4.31387 ( 3) link_NAG-ASN : bond 0.00265 ( 2) link_NAG-ASN : angle 2.44484 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8717 (tpt) cc_final: 0.8374 (tpp) REVERT: A 176 MET cc_start: 0.7926 (tpp) cc_final: 0.7452 (tpp) REVERT: A 254 TRP cc_start: 0.7838 (t-100) cc_final: 0.7387 (t60) REVERT: A 356 PHE cc_start: 0.7232 (m-80) cc_final: 0.6694 (t80) REVERT: A 381 ILE cc_start: 0.8555 (tp) cc_final: 0.8231 (tp) outliers start: 12 outliers final: 11 residues processed: 81 average time/residue: 0.0603 time to fit residues: 6.5686 Evaluate side-chains 85 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 50.0000 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 40.0000 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 365 GLN ** 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 = 0.3755 r_free = 0.3755 target = 0.166751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.121158 restraints weight = 4860.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.117880 restraints weight = 4206.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.118942 restraints weight = 3958.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.119378 restraints weight = 3524.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.119541 restraints weight = 3162.073| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4388 Z= 0.150 Angle : 0.634 7.887 5974 Z= 0.306 Chirality : 0.043 0.283 695 Planarity : 0.003 0.033 726 Dihedral : 6.337 73.144 680 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.92 % Allowed : 22.14 % Favored : 74.94 % 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: 1.25 (0.36), residues: 562 helix: 1.89 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.01 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 526 TYR 0.022 0.001 TYR A 590 PHE 0.016 0.001 PHE A 224 TRP 0.004 0.001 TRP A 171 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4378) covalent geometry : angle 0.62006 ( 5951) SS BOND : bond 0.00101 ( 7) SS BOND : angle 1.37913 ( 14) hydrogen bonds : bond 0.03953 ( 263) hydrogen bonds : angle 4.07088 ( 777) link_BETA1-4 : bond 0.00591 ( 1) link_BETA1-4 : angle 4.24129 ( 3) link_NAG-ASN : bond 0.00268 ( 2) link_NAG-ASN : angle 2.38385 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 900.62 seconds wall clock time: 16 minutes 14.66 seconds (974.66 seconds total)