Starting phenix.real_space_refine on Tue Feb 3 14:01:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kvj_62596/02_2026/9kvj_62596.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kvj_62596/02_2026/9kvj_62596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kvj_62596/02_2026/9kvj_62596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kvj_62596/02_2026/9kvj_62596.map" model { file = "/net/cci-nas-00/data/ceres_data/9kvj_62596/02_2026/9kvj_62596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kvj_62596/02_2026/9kvj_62596.cif" } resolution = 3.82 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= 0.009 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 15 5.16 5 C 2128 2.51 5 N 552 2.21 5 O 647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3342 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "G" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1529 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 11, 'TRANS': 180} Chain breaks: 1 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 0.60, per 1000 atoms: 0.18 Number of scatterers: 3342 At special positions: 0 Unit cell: (86.358, 76.244, 76.244, 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 15 16.00 O 647 8.00 N 552 7.00 C 2128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.04 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 A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " BETA1-6 " NAG A 1 " - " FUC A 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN G 343 " Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 83.7 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 10.0% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.807A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.672A pdb=" N PHE D 83 " --> pdb=" O THR D 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 343 Processing helix chain 'G' and resid 365 through 371 removed outlier: 3.879A pdb=" N PHE G 371 " --> pdb=" O VAL G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 388 removed outlier: 4.303A pdb=" N ASN G 388 " --> pdb=" O THR G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 410 removed outlier: 3.865A pdb=" N VAL G 407 " --> pdb=" O GLY G 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER G 408 " --> pdb=" O ASN G 405 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN G 409 " --> pdb=" O GLU G 406 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE G 410 " --> pdb=" O VAL G 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 404 through 410' Processing helix chain 'G' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.676A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.676A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR C 78 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.717A pdb=" N THR C 116 " --> pdb=" O GLU C 10 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 98 through 99 removed outlier: 4.599A pdb=" N VAL C 108 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.767A pdb=" N SER D 22 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER D 63 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.880A pdb=" N VAL D 13 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY D 84 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU D 33 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LYS D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 354 through 358 removed outlier: 3.738A pdb=" N ASN G 354 " --> pdb=" O SER G 399 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER G 514 " --> pdb=" O TYR G 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 452 through 454 82 hydrogen bonds defined for protein. 189 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: 0.36 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1049 1.34 - 1.46: 864 1.46 - 1.58: 1501 1.58 - 1.70: 0 1.70 - 1.82: 17 Bond restraints: 3431 Sorted by residual: bond pdb=" N ALA G 372 " pdb=" CA ALA G 372 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.41e-02 5.03e+03 2.37e+00 bond pdb=" CA ASN G 343 " pdb=" CB ASN G 343 " ideal model delta sigma weight residual 1.525 1.545 -0.020 1.36e-02 5.41e+03 2.23e+00 bond pdb=" C2 BMA A 3 " pdb=" O2 BMA A 3 " ideal model delta sigma weight residual 1.402 1.432 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" CA ALA G 372 " pdb=" C ALA G 372 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.26e-02 6.30e+03 2.15e+00 bond pdb=" C2 BMA A 3 " pdb=" C3 BMA A 3 " ideal model delta sigma weight residual 1.544 1.518 0.026 2.00e-02 2.50e+03 1.74e+00 ... (remaining 3426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 4629 3.05 - 6.10: 35 6.10 - 9.15: 1 9.15 - 12.20: 0 12.20 - 15.25: 1 Bond angle restraints: 4666 Sorted by residual: angle pdb=" N ALA G 372 " pdb=" CA ALA G 372 " pdb=" C ALA G 372 " ideal model delta sigma weight residual 109.81 125.06 -15.25 2.21e+00 2.05e-01 4.76e+01 angle pdb=" C LEU G 335 " pdb=" N CYS G 336 " pdb=" CA CYS G 336 " ideal model delta sigma weight residual 123.56 115.47 8.09 1.98e+00 2.55e-01 1.67e+01 angle pdb=" N ASN G 370 " pdb=" CA ASN G 370 " pdb=" C ASN G 370 " ideal model delta sigma weight residual 111.71 115.03 -3.32 1.15e+00 7.56e-01 8.33e+00 angle pdb=" N PRO G 373 " pdb=" CA PRO G 373 " pdb=" C PRO G 373 " ideal model delta sigma weight residual 112.47 117.97 -5.50 2.06e+00 2.36e-01 7.14e+00 angle pdb=" C GLY C 56 " pdb=" N GLU C 57 " pdb=" CA GLU C 57 " ideal model delta sigma weight residual 121.20 117.59 3.61 1.40e+00 5.10e-01 6.64e+00 ... (remaining 4661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.60: 1924 21.60 - 43.21: 107 43.21 - 64.81: 8 64.81 - 86.42: 8 86.42 - 108.02: 4 Dihedral angle restraints: 2051 sinusoidal: 846 harmonic: 1205 Sorted by residual: dihedral pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " pdb=" CB CYS G 361 " ideal model delta sinusoidal sigma weight residual 93.00 24.07 68.93 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CA PRO G 337 " pdb=" C PRO G 337 " pdb=" N PHE G 338 " pdb=" CA PHE G 338 " ideal model delta harmonic sigma weight residual 180.00 156.68 23.32 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CB CYS G 480 " pdb=" SG CYS G 480 " pdb=" SG CYS G 488 " pdb=" CB CYS G 488 " ideal model delta sinusoidal sigma weight residual -86.00 -122.51 36.51 1 1.00e+01 1.00e-02 1.88e+01 ... (remaining 2048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 477 0.097 - 0.194: 27 0.194 - 0.291: 2 0.291 - 0.388: 1 0.388 - 0.485: 1 Chirality restraints: 508 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-02 2.50e+03 2.75e+02 chirality pdb=" C1 FUC A 4 " pdb=" O6 NAG A 1 " pdb=" C2 FUC A 4 " pdb=" O5 FUC A 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.29e+01 chirality pdb=" CA ALA G 372 " pdb=" N ALA G 372 " pdb=" C ALA G 372 " pdb=" CB ALA G 372 " both_signs ideal model delta sigma weight residual False 2.48 2.00 0.48 2.00e-01 2.50e+01 5.88e+00 ... (remaining 505 not shown) Planarity restraints: 598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.159 2.00e-02 2.50e+03 1.31e-01 2.14e+02 pdb=" C7 NAG A 1 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.119 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.209 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " -0.046 2.00e-02 2.50e+03 3.77e-02 1.77e+01 pdb=" C7 NAG A 2 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " 0.060 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 368 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.94e+00 pdb=" C LEU G 368 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU G 368 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR G 369 " 0.010 2.00e-02 2.50e+03 ... (remaining 595 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 123 2.70 - 3.25: 3160 3.25 - 3.80: 4884 3.80 - 4.35: 6194 4.35 - 4.90: 10488 Nonbonded interactions: 24849 Sorted by model distance: nonbonded pdb=" OG1 THR D 14 " pdb=" OD2 ASP D 17 " model vdw 2.149 3.040 nonbonded pdb=" O SER D 7 " pdb=" OG SER D 22 " model vdw 2.187 3.040 nonbonded pdb=" NH1 ARG G 457 " pdb=" OD2 ASP G 467 " model vdw 2.249 3.120 nonbonded pdb=" OD2 ASP G 398 " pdb=" OH TYR G 423 " model vdw 2.268 3.040 nonbonded pdb=" O ASN D 92 " pdb=" OG1 THR G 345 " model vdw 2.321 3.040 ... (remaining 24844 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: 13.850 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.410 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 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 : 0.005 0.030 3440 Z= 0.228 Angle : 0.800 15.836 4688 Z= 0.432 Chirality : 0.055 0.485 508 Planarity : 0.007 0.131 597 Dihedral : 14.408 108.025 1270 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.54 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.34 (0.35), residues: 410 helix: -4.61 (0.43), residues: 20 sheet: -2.75 (0.42), residues: 132 loop : -2.92 (0.32), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 454 TYR 0.008 0.001 TYR G 453 PHE 0.009 0.001 PHE G 342 TRP 0.013 0.001 TRP G 436 HIS 0.001 0.000 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 3431) covalent geometry : angle 0.75544 ( 4666) SS BOND : bond 0.00405 ( 5) SS BOND : angle 2.00695 ( 10) hydrogen bonds : bond 0.30911 ( 74) hydrogen bonds : angle 11.49052 ( 189) link_BETA1-4 : bond 0.00177 ( 2) link_BETA1-4 : angle 1.83757 ( 6) link_BETA1-6 : bond 0.00626 ( 1) link_BETA1-6 : angle 1.74761 ( 3) link_NAG-ASN : bond 0.02443 ( 1) link_NAG-ASN : angle 9.42897 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 GLU cc_start: 0.8665 (pt0) cc_final: 0.8416 (pt0) REVERT: D 24 ARG cc_start: 0.7153 (mtt-85) cc_final: 0.6869 (ptp-110) REVERT: D 103 LYS cc_start: 0.7356 (ptpt) cc_final: 0.7053 (ttmm) REVERT: G 340 GLU cc_start: 0.8646 (tt0) cc_final: 0.8331 (tt0) REVERT: G 417 ASN cc_start: 0.7420 (m-40) cc_final: 0.7040 (t0) REVERT: G 420 ASP cc_start: 0.7043 (m-30) cc_final: 0.6779 (m-30) REVERT: G 422 ASN cc_start: 0.7648 (m110) cc_final: 0.7250 (m110) REVERT: G 461 LEU cc_start: 0.8792 (mt) cc_final: 0.8583 (mt) REVERT: G 474 GLN cc_start: 0.7412 (pp30) cc_final: 0.7158 (pt0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0666 time to fit residues: 8.4814 Evaluate side-chains 72 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.0000 chunk 22 optimal weight: 0.0770 chunk 37 optimal weight: 0.5980 overall best weight: 0.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 1 GLN C 6 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN D 27 GLN D 31 ASN D 107 ASN G 394 ASN ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 460 ASN G 505 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.116083 restraints weight = 5337.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119358 restraints weight = 3346.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.121566 restraints weight = 2436.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123110 restraints weight = 1946.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124111 restraints weight = 1654.917| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3440 Z= 0.140 Angle : 0.642 7.223 4688 Z= 0.329 Chirality : 0.044 0.137 508 Planarity : 0.005 0.055 597 Dihedral : 9.125 64.445 535 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.79 % Allowed : 12.53 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.37), residues: 410 helix: -4.22 (0.58), residues: 20 sheet: -1.87 (0.44), residues: 130 loop : -2.50 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 45 TYR 0.012 0.001 TYR C 32 PHE 0.012 0.001 PHE G 342 TRP 0.010 0.001 TRP G 436 HIS 0.002 0.001 HIS G 505 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3431) covalent geometry : angle 0.61908 ( 4666) SS BOND : bond 0.00625 ( 5) SS BOND : angle 1.53391 ( 10) hydrogen bonds : bond 0.04099 ( 74) hydrogen bonds : angle 6.41465 ( 189) link_BETA1-4 : bond 0.00875 ( 2) link_BETA1-4 : angle 2.28018 ( 6) link_BETA1-6 : bond 0.00064 ( 1) link_BETA1-6 : angle 1.70770 ( 3) link_NAG-ASN : bond 0.00151 ( 1) link_NAG-ASN : angle 5.25635 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 3 GLN cc_start: 0.8312 (pm20) cc_final: 0.7955 (pm20) REVERT: C 90 ASP cc_start: 0.8731 (p0) cc_final: 0.8228 (p0) REVERT: G 362 VAL cc_start: 0.9307 (OUTLIER) cc_final: 0.9069 (m) outliers start: 10 outliers final: 8 residues processed: 91 average time/residue: 0.0364 time to fit residues: 4.1629 Evaluate side-chains 80 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.0040 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.0670 overall best weight: 0.2728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN D 6 GLN D 31 ASN ** G 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.116166 restraints weight = 5356.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119347 restraints weight = 3344.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.121476 restraints weight = 2429.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123119 restraints weight = 1936.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.124075 restraints weight = 1626.748| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3440 Z= 0.118 Angle : 0.628 7.651 4688 Z= 0.311 Chirality : 0.045 0.176 508 Planarity : 0.005 0.054 597 Dihedral : 7.215 44.944 535 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.67 % Allowed : 16.71 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.38), residues: 410 helix: -3.78 (0.76), residues: 20 sheet: -1.43 (0.45), residues: 130 loop : -2.36 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 98 TYR 0.023 0.001 TYR C 32 PHE 0.011 0.001 PHE D 62 TRP 0.011 0.001 TRP G 436 HIS 0.001 0.001 HIS G 505 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3431) covalent geometry : angle 0.60643 ( 4666) SS BOND : bond 0.00271 ( 5) SS BOND : angle 1.33338 ( 10) hydrogen bonds : bond 0.03266 ( 74) hydrogen bonds : angle 5.65526 ( 189) link_BETA1-4 : bond 0.00638 ( 2) link_BETA1-4 : angle 2.31186 ( 6) link_BETA1-6 : bond 0.00013 ( 1) link_BETA1-6 : angle 1.61593 ( 3) link_NAG-ASN : bond 0.00308 ( 1) link_NAG-ASN : angle 4.98545 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 3 GLN cc_start: 0.8336 (pm20) cc_final: 0.7977 (pm20) REVERT: C 90 ASP cc_start: 0.8774 (p0) cc_final: 0.8086 (p0) REVERT: C 98 ARG cc_start: 0.8785 (ttp-170) cc_final: 0.7813 (ttp-170) outliers start: 6 outliers final: 5 residues processed: 79 average time/residue: 0.0687 time to fit residues: 6.6334 Evaluate side-chains 71 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN D 31 ASN G 394 ASN ** G 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.131865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.110986 restraints weight = 5346.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.114127 restraints weight = 3377.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116309 restraints weight = 2477.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117676 restraints weight = 1985.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118831 restraints weight = 1705.961| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 3440 Z= 0.183 Angle : 0.640 7.494 4688 Z= 0.319 Chirality : 0.045 0.128 508 Planarity : 0.005 0.056 597 Dihedral : 6.157 35.260 535 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.06 % Allowed : 15.88 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.39), residues: 410 helix: -3.88 (0.71), residues: 20 sheet: -1.38 (0.44), residues: 140 loop : -2.20 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 67 TYR 0.014 0.001 TYR C 32 PHE 0.009 0.001 PHE C 70 TRP 0.012 0.001 TRP G 436 HIS 0.001 0.001 HIS G 505 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 3431) covalent geometry : angle 0.61699 ( 4666) SS BOND : bond 0.00331 ( 5) SS BOND : angle 1.45842 ( 10) hydrogen bonds : bond 0.03201 ( 74) hydrogen bonds : angle 5.40008 ( 189) link_BETA1-4 : bond 0.00526 ( 2) link_BETA1-4 : angle 2.17355 ( 6) link_BETA1-6 : bond 0.00373 ( 1) link_BETA1-6 : angle 2.22571 ( 3) link_NAG-ASN : bond 0.00197 ( 1) link_NAG-ASN : angle 5.14741 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 3 GLN cc_start: 0.8380 (pm20) cc_final: 0.8042 (pm20) REVERT: C 90 ASP cc_start: 0.8775 (p0) cc_final: 0.8023 (p0) REVERT: G 355 ARG cc_start: 0.8776 (ttt90) cc_final: 0.8415 (ttt90) outliers start: 11 outliers final: 10 residues processed: 87 average time/residue: 0.0553 time to fit residues: 5.7474 Evaluate side-chains 83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 0.0170 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 0.0020 chunk 21 optimal weight: 0.9980 overall best weight: 0.2626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN D 31 ASN G 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113742 restraints weight = 5346.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116986 restraints weight = 3335.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119142 restraints weight = 2427.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120702 restraints weight = 1937.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121656 restraints weight = 1643.828| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3440 Z= 0.115 Angle : 0.604 6.406 4688 Z= 0.300 Chirality : 0.043 0.135 508 Planarity : 0.005 0.054 597 Dihedral : 5.359 31.556 535 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.79 % Allowed : 18.94 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.40), residues: 410 helix: -3.64 (0.81), residues: 20 sheet: -1.14 (0.45), residues: 134 loop : -2.05 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 346 TYR 0.013 0.001 TYR C 105 PHE 0.018 0.001 PHE C 64 TRP 0.012 0.001 TRP G 436 HIS 0.001 0.000 HIS G 505 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3431) covalent geometry : angle 0.58648 ( 4666) SS BOND : bond 0.00249 ( 5) SS BOND : angle 1.14551 ( 10) hydrogen bonds : bond 0.02736 ( 74) hydrogen bonds : angle 5.12338 ( 189) link_BETA1-4 : bond 0.00662 ( 2) link_BETA1-4 : angle 1.96785 ( 6) link_BETA1-6 : bond 0.00017 ( 1) link_BETA1-6 : angle 1.62273 ( 3) link_NAG-ASN : bond 0.00238 ( 1) link_NAG-ASN : angle 4.51164 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 GLN cc_start: 0.8353 (pm20) cc_final: 0.7997 (pm20) REVERT: C 90 ASP cc_start: 0.8750 (p0) cc_final: 0.8010 (p0) REVERT: C 98 ARG cc_start: 0.8735 (ttp-170) cc_final: 0.7676 (ttp-170) REVERT: D 11 LEU cc_start: 0.7979 (mt) cc_final: 0.7721 (mp) outliers start: 10 outliers final: 8 residues processed: 86 average time/residue: 0.0519 time to fit residues: 5.4562 Evaluate side-chains 79 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.0270 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN D 31 ASN G 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113898 restraints weight = 5335.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117147 restraints weight = 3305.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.119328 restraints weight = 2393.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120792 restraints weight = 1904.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121706 restraints weight = 1619.996| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3440 Z= 0.122 Angle : 0.594 6.288 4688 Z= 0.297 Chirality : 0.043 0.125 508 Planarity : 0.005 0.054 597 Dihedral : 5.079 24.955 535 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.62 % Allowed : 18.66 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.40), residues: 410 helix: -3.70 (0.81), residues: 20 sheet: -0.82 (0.48), residues: 124 loop : -2.03 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 346 TYR 0.013 0.001 TYR C 105 PHE 0.015 0.001 PHE C 64 TRP 0.011 0.001 TRP G 436 HIS 0.001 0.000 HIS G 505 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3431) covalent geometry : angle 0.57679 ( 4666) SS BOND : bond 0.00232 ( 5) SS BOND : angle 1.30230 ( 10) hydrogen bonds : bond 0.02615 ( 74) hydrogen bonds : angle 5.02241 ( 189) link_BETA1-4 : bond 0.00613 ( 2) link_BETA1-4 : angle 1.74424 ( 6) link_BETA1-6 : bond 0.00016 ( 1) link_BETA1-6 : angle 1.74955 ( 3) link_NAG-ASN : bond 0.00225 ( 1) link_NAG-ASN : angle 4.41948 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 GLN cc_start: 0.8344 (pm20) cc_final: 0.8060 (pm20) REVERT: C 90 ASP cc_start: 0.8704 (p0) cc_final: 0.8013 (p0) REVERT: D 11 LEU cc_start: 0.8151 (mt) cc_final: 0.7880 (mp) REVERT: G 355 ARG cc_start: 0.8736 (ttt90) cc_final: 0.8419 (ttt90) REVERT: G 357 ARG cc_start: 0.7826 (ttt90) cc_final: 0.7584 (mtp85) outliers start: 13 outliers final: 12 residues processed: 78 average time/residue: 0.0747 time to fit residues: 7.0773 Evaluate side-chains 79 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN C 39 GLN D 31 ASN G 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.133255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112534 restraints weight = 5506.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115628 restraints weight = 3471.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117564 restraints weight = 2551.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119135 restraints weight = 2069.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119882 restraints weight = 1765.741| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 3440 Z= 0.185 Angle : 0.630 7.091 4688 Z= 0.312 Chirality : 0.044 0.127 508 Planarity : 0.005 0.057 597 Dihedral : 5.160 21.373 535 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.18 % Allowed : 18.11 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.40), residues: 410 helix: -3.88 (0.71), residues: 20 sheet: -0.85 (0.48), residues: 124 loop : -1.97 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 346 TYR 0.017 0.001 TYR C 32 PHE 0.011 0.001 PHE C 64 TRP 0.012 0.001 TRP G 436 HIS 0.001 0.001 HIS G 505 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 3431) covalent geometry : angle 0.61007 ( 4666) SS BOND : bond 0.00306 ( 5) SS BOND : angle 1.50095 ( 10) hydrogen bonds : bond 0.02905 ( 74) hydrogen bonds : angle 5.12027 ( 189) link_BETA1-4 : bond 0.00540 ( 2) link_BETA1-4 : angle 1.62409 ( 6) link_BETA1-6 : bond 0.00384 ( 1) link_BETA1-6 : angle 2.22915 ( 3) link_NAG-ASN : bond 0.00144 ( 1) link_NAG-ASN : angle 4.82463 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 3 GLN cc_start: 0.8364 (pm20) cc_final: 0.8025 (pm20) REVERT: C 32 TYR cc_start: 0.8206 (m-10) cc_final: 0.8004 (m-10) REVERT: C 90 ASP cc_start: 0.8699 (p0) cc_final: 0.7978 (p0) REVERT: C 98 ARG cc_start: 0.8784 (ttp-170) cc_final: 0.7790 (ttp-170) REVERT: D 11 LEU cc_start: 0.8227 (mt) cc_final: 0.7927 (mp) REVERT: D 76 ASN cc_start: 0.6918 (p0) cc_final: 0.6667 (p0) outliers start: 15 outliers final: 14 residues processed: 79 average time/residue: 0.0656 time to fit residues: 6.3977 Evaluate side-chains 81 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 0.0010 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN D 31 ASN ** G 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113974 restraints weight = 5469.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117166 restraints weight = 3408.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119335 restraints weight = 2480.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120697 restraints weight = 1985.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121780 restraints weight = 1703.815| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3440 Z= 0.139 Angle : 0.622 8.402 4688 Z= 0.305 Chirality : 0.044 0.143 508 Planarity : 0.005 0.053 597 Dihedral : 5.020 21.324 535 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.90 % Allowed : 18.94 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.40), residues: 410 helix: -3.92 (0.69), residues: 20 sheet: -0.78 (0.48), residues: 124 loop : -1.97 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 346 TYR 0.013 0.001 TYR C 32 PHE 0.031 0.002 PHE G 456 TRP 0.013 0.001 TRP G 436 HIS 0.001 0.000 HIS G 505 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 3431) covalent geometry : angle 0.60545 ( 4666) SS BOND : bond 0.00294 ( 5) SS BOND : angle 1.33227 ( 10) hydrogen bonds : bond 0.02688 ( 74) hydrogen bonds : angle 5.00912 ( 189) link_BETA1-4 : bond 0.00528 ( 2) link_BETA1-4 : angle 1.56960 ( 6) link_BETA1-6 : bond 0.00221 ( 1) link_BETA1-6 : angle 1.81971 ( 3) link_NAG-ASN : bond 0.00191 ( 1) link_NAG-ASN : angle 4.55399 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 3 GLN cc_start: 0.8349 (pm20) cc_final: 0.8050 (pm20) REVERT: C 90 ASP cc_start: 0.8626 (p0) cc_final: 0.7921 (p0) REVERT: D 11 LEU cc_start: 0.8200 (mt) cc_final: 0.7885 (mp) REVERT: D 76 ASN cc_start: 0.6945 (p0) cc_final: 0.6625 (p0) REVERT: G 357 ARG cc_start: 0.7850 (ttt90) cc_final: 0.7593 (mtp85) REVERT: G 472 ILE cc_start: 0.6754 (mm) cc_final: 0.6533 (mm) REVERT: G 501 TYR cc_start: 0.6180 (OUTLIER) cc_final: 0.5361 (m-80) outliers start: 14 outliers final: 13 residues processed: 77 average time/residue: 0.0677 time to fit residues: 6.4306 Evaluate side-chains 79 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 501 TYR Chi-restraints excluded: chain G residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN D 31 ASN G 394 ASN G 474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.112135 restraints weight = 5462.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.115239 restraints weight = 3442.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117342 restraints weight = 2522.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118795 restraints weight = 2026.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.119609 restraints weight = 1735.316| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3440 Z= 0.162 Angle : 0.660 10.906 4688 Z= 0.320 Chirality : 0.044 0.212 508 Planarity : 0.005 0.059 597 Dihedral : 5.086 20.948 535 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.46 % Allowed : 18.66 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.40), residues: 410 helix: -4.00 (0.67), residues: 20 sheet: -0.74 (0.49), residues: 124 loop : -1.97 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 346 TYR 0.020 0.001 TYR C 32 PHE 0.013 0.001 PHE C 64 TRP 0.013 0.001 TRP G 436 HIS 0.001 0.001 HIS G 505 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 3431) covalent geometry : angle 0.64288 ( 4666) SS BOND : bond 0.00300 ( 5) SS BOND : angle 1.45387 ( 10) hydrogen bonds : bond 0.02808 ( 74) hydrogen bonds : angle 5.02957 ( 189) link_BETA1-4 : bond 0.00602 ( 2) link_BETA1-4 : angle 1.53195 ( 6) link_BETA1-6 : bond 0.00266 ( 1) link_BETA1-6 : angle 2.04187 ( 3) link_NAG-ASN : bond 0.00184 ( 1) link_NAG-ASN : angle 4.59829 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 3 GLN cc_start: 0.8336 (pm20) cc_final: 0.8044 (pm20) REVERT: C 90 ASP cc_start: 0.8608 (p0) cc_final: 0.7911 (p0) REVERT: D 76 ASN cc_start: 0.7011 (p0) cc_final: 0.6687 (p0) REVERT: G 501 TYR cc_start: 0.6224 (OUTLIER) cc_final: 0.5400 (m-80) outliers start: 16 outliers final: 14 residues processed: 78 average time/residue: 0.0550 time to fit residues: 5.3704 Evaluate side-chains 81 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 394 ASN Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 501 TYR Chi-restraints excluded: chain G residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN G 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110453 restraints weight = 5461.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113719 restraints weight = 3345.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.115892 restraints weight = 2408.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117363 restraints weight = 1921.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118421 restraints weight = 1637.633| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 3440 Z= 0.195 Angle : 0.666 8.688 4688 Z= 0.336 Chirality : 0.044 0.147 508 Planarity : 0.005 0.060 597 Dihedral : 5.178 21.002 535 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.18 % Allowed : 19.50 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.40), residues: 410 helix: -4.05 (0.64), residues: 20 sheet: -0.75 (0.49), residues: 124 loop : -1.95 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 98 TYR 0.026 0.002 TYR C 32 PHE 0.013 0.002 PHE G 456 TRP 0.013 0.001 TRP G 436 HIS 0.001 0.000 HIS G 505 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 3431) covalent geometry : angle 0.64802 ( 4666) SS BOND : bond 0.00310 ( 5) SS BOND : angle 1.63404 ( 10) hydrogen bonds : bond 0.02913 ( 74) hydrogen bonds : angle 5.06986 ( 189) link_BETA1-4 : bond 0.00554 ( 2) link_BETA1-4 : angle 1.54253 ( 6) link_BETA1-6 : bond 0.00453 ( 1) link_BETA1-6 : angle 2.19391 ( 3) link_NAG-ASN : bond 0.00213 ( 1) link_NAG-ASN : angle 4.70015 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 3 GLN cc_start: 0.8343 (pm20) cc_final: 0.8009 (pm20) REVERT: C 87 LYS cc_start: 0.8827 (mttt) cc_final: 0.8574 (mttt) REVERT: C 90 ASP cc_start: 0.8654 (p0) cc_final: 0.7960 (p0) REVERT: D 76 ASN cc_start: 0.7108 (p0) cc_final: 0.6792 (p0) REVERT: G 501 TYR cc_start: 0.6257 (OUTLIER) cc_final: 0.5520 (m-80) outliers start: 15 outliers final: 12 residues processed: 75 average time/residue: 0.0730 time to fit residues: 6.5322 Evaluate side-chains 79 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 501 TYR Chi-restraints excluded: chain G residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.109855 restraints weight = 5568.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113106 restraints weight = 3431.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115301 restraints weight = 2487.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.116801 restraints weight = 1994.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117658 restraints weight = 1702.838| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 3440 Z= 0.177 Angle : 0.662 8.572 4688 Z= 0.329 Chirality : 0.044 0.129 508 Planarity : 0.005 0.057 597 Dihedral : 5.203 21.279 535 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.62 % Allowed : 20.61 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.40), residues: 410 helix: -4.05 (0.63), residues: 20 sheet: -0.39 (0.52), residues: 112 loop : -1.96 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 98 TYR 0.013 0.001 TYR C 105 PHE 0.010 0.001 PHE C 64 TRP 0.013 0.001 TRP G 436 HIS 0.001 0.001 HIS G 505 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 3431) covalent geometry : angle 0.64448 ( 4666) SS BOND : bond 0.00291 ( 5) SS BOND : angle 1.56822 ( 10) hydrogen bonds : bond 0.02855 ( 74) hydrogen bonds : angle 5.07309 ( 189) link_BETA1-4 : bond 0.00596 ( 2) link_BETA1-4 : angle 1.55041 ( 6) link_BETA1-6 : bond 0.00374 ( 1) link_BETA1-6 : angle 2.09429 ( 3) link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 4.61015 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 981.21 seconds wall clock time: 17 minutes 38.65 seconds (1058.65 seconds total)