Starting phenix.real_space_refine on Tue Aug 4 13:40:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uhf_64162/08_2026/9uhf_64162.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uhf_64162/08_2026/9uhf_64162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uhf_64162/08_2026/9uhf_64162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uhf_64162/08_2026/9uhf_64162.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uhf_64162/08_2026/9uhf_64162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uhf_64162/08_2026/9uhf_64162.map" } resolution = 4.18 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2138 2.51 5 N 565 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3368 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1588 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 13, 'TRANS': 184} Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 909 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "M" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 0.84, per 1000 atoms: 0.25 Number of scatterers: 3368 At special positions: 0 Unit cell: (63.13, 84.53, 97.37, 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 17 16.00 O 648 8.00 N 565 7.00 C 2138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " 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 601 " - " ASN A 354 " " NAG B 1 " - " ASN A 343 " Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 157.4 milliseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 7 sheets defined 11.1% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.955A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.154A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.731A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.611A pdb=" N VAL A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.312A pdb=" N ASN I 32 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.986A pdb=" N ILE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.157A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.741A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.996A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.515A pdb=" N VAL I 5 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP I 72 " --> pdb=" O THR I 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 11 through 12 removed outlier: 7.221A pdb=" N ILE I 12 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N THR I 116 " --> pdb=" O ILE I 12 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR I 113 " --> pdb=" O TYR I 93 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N MET I 34 " --> pdb=" O LEU I 50 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 5 through 7 removed outlier: 3.744A pdb=" N VAL M 19 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE M 21 " --> pdb=" O PHE M 73 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE M 71 " --> pdb=" O CYS M 23 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER M 67 " --> pdb=" O GLU M 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.691A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA M 84 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 186 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: 0.29 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1071 1.35 - 1.47: 927 1.47 - 1.59: 1433 1.59 - 1.71: 0 1.71 - 1.83: 22 Bond restraints: 3453 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" CA ILE A 468 " pdb=" CB ILE A 468 " ideal model delta sigma weight residual 1.533 1.545 -0.013 1.20e-02 6.94e+03 1.12e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.433 -0.020 2.00e-02 2.50e+03 1.03e+00 ... (remaining 3448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 4595 2.15 - 4.30: 80 4.30 - 6.45: 11 6.45 - 8.60: 0 8.60 - 10.75: 1 Bond angle restraints: 4687 Sorted by residual: angle pdb=" N ILE M 29 " pdb=" CA ILE M 29 " pdb=" C ILE M 29 " ideal model delta sigma weight residual 112.43 106.10 6.33 9.20e-01 1.18e+00 4.73e+01 angle pdb=" CA GLY A 431 " pdb=" C GLY A 431 " pdb=" N CYS A 432 " ideal model delta sigma weight residual 114.75 118.32 -3.57 9.90e-01 1.02e+00 1.30e+01 angle pdb=" CB MET M 4 " pdb=" CG MET M 4 " pdb=" SD MET M 4 " ideal model delta sigma weight residual 112.70 123.45 -10.75 3.00e+00 1.11e-01 1.28e+01 angle pdb=" CA GLY A 431 " pdb=" C GLY A 431 " pdb=" O GLY A 431 " ideal model delta sigma weight residual 122.16 119.46 2.70 8.20e-01 1.49e+00 1.08e+01 angle pdb=" C PRO A 486 " pdb=" N ASN A 487 " pdb=" CA ASN A 487 " ideal model delta sigma weight residual 121.54 126.27 -4.73 1.91e+00 2.74e-01 6.12e+00 ... (remaining 4682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.46: 1912 21.46 - 42.93: 128 42.93 - 64.39: 13 64.39 - 85.86: 14 85.86 - 107.32: 12 Dihedral angle restraints: 2079 sinusoidal: 854 harmonic: 1225 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -158.90 72.90 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -147.45 61.45 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CA ASN A 360 " pdb=" C ASN A 360 " pdb=" N CYS A 361 " pdb=" CA CYS A 361 " ideal model delta harmonic sigma weight residual 180.00 -157.76 -22.24 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 2076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 341 0.039 - 0.078: 111 0.078 - 0.116: 45 0.116 - 0.155: 8 0.155 - 0.194: 4 Chirality restraints: 509 Sorted by residual: chirality pdb=" CB ILE A 468 " pdb=" CA ILE A 468 " pdb=" CG1 ILE A 468 " pdb=" CG2 ILE A 468 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 354 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 506 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE M 29 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" C ILE M 29 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE M 29 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN M 30 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 521 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN M 79 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO M 80 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO M 80 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO M 80 " 0.016 5.00e-02 4.00e+02 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 575 2.77 - 3.30: 3197 3.30 - 3.84: 5269 3.84 - 4.37: 5952 4.37 - 4.90: 10104 Nonbonded interactions: 25097 Sorted by model distance: nonbonded pdb=" OG1 THR A 430 " pdb=" O PHE A 515 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR M 22 " pdb=" OE1 GLU M 70 " model vdw 2.278 3.040 nonbonded pdb=" OD2 ASP A 442 " pdb=" NH2 ARG A 509 " model vdw 2.290 3.120 nonbonded pdb=" OH TYR A 473 " pdb=" O ARG I 31 " model vdw 2.302 3.040 nonbonded pdb=" O TRP A 353 " pdb=" NH2 ARG A 466 " model vdw 2.318 3.120 ... (remaining 25092 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: 1.410 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: 0.010 Set scattering table: 0.000 Process input model: 3.940 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 : 0.003 0.028 3461 Z= 0.142 Angle : 0.683 10.752 4706 Z= 0.371 Chirality : 0.047 0.194 509 Planarity : 0.004 0.043 601 Dihedral : 17.783 107.324 1288 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.39), residues: 418 helix: -2.97 (1.04), residues: 20 sheet: -0.38 (0.48), residues: 119 loop : -1.11 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 66 TYR 0.015 0.001 TYR A 495 PHE 0.018 0.001 PHE A 377 TRP 0.006 0.001 TRP M 35 HIS 0.001 0.000 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 3453) covalent geometry : angle 0.67482 / 0.37 ( 4687) SS BOND : bond 0.00482 / 0.24 ( 5) SS BOND : angle 1.88068 / 1.01 ( 10) hydrogen bonds : bond 0.29083 / 19.90 ( 71) hydrogen bonds : angle 10.32545 / 7.03 ( 186) link_BETA1-4 : bond 0.00232 / 0.12 ( 1) link_BETA1-4 : angle 1.43797 / 0.81 ( 3) link_NAG-ASN : bond 0.00035 / 0.02 ( 2) link_NAG-ASN : angle 1.66603 / 0.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 32 TYR cc_start: 0.8040 (m-80) cc_final: 0.7790 (m-80) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0608 time to fit residues: 5.3671 Evaluate side-chains 51 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.086 ------------------------------------------------------------------------------- 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: 0.8980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.088744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.077476 restraints weight = 13763.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.079153 restraints weight = 9362.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.080369 restraints weight = 7048.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.081215 restraints weight = 5707.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.081876 restraints weight = 4872.160| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3461 Z= 0.145 Angle : 0.631 8.093 4706 Z= 0.318 Chirality : 0.047 0.228 509 Planarity : 0.004 0.042 601 Dihedral : 12.497 76.763 532 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.39), residues: 418 helix: -2.98 (1.00), residues: 20 sheet: -0.45 (0.47), residues: 129 loop : -1.15 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 466 TYR 0.016 0.001 TYR A 495 PHE 0.010 0.002 PHE A 377 TRP 0.006 0.001 TRP A 353 HIS 0.002 0.001 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 3453) covalent geometry : angle 0.61898 / 0.31 ( 4687) SS BOND : bond 0.00832 / 0.42 ( 5) SS BOND : angle 1.37676 / 0.73 ( 10) hydrogen bonds : bond 0.04234 / 2.88 ( 71) hydrogen bonds : angle 7.18010 / 4.99 ( 186) link_BETA1-4 : bond 0.00556 / 0.29 ( 1) link_BETA1-4 : angle 2.36777 / 1.24 ( 3) link_NAG-ASN : bond 0.00485 / 0.25 ( 2) link_NAG-ASN : angle 2.57249 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 103 LYS cc_start: 0.7756 (tptp) cc_final: 0.7399 (tptp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0416 time to fit residues: 4.0636 Evaluate side-chains 54 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 GLN I 76 ASN ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 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 = 0.3513 r_free = 0.3513 target = 0.085159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074082 restraints weight = 14093.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.075718 restraints weight = 9497.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.076836 restraints weight = 7128.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.077673 restraints weight = 5818.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078178 restraints weight = 4953.177| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3461 Z= 0.240 Angle : 0.761 10.125 4706 Z= 0.385 Chirality : 0.049 0.216 509 Planarity : 0.005 0.042 601 Dihedral : 9.132 53.782 532 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.55 % Allowed : 4.93 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.38), residues: 418 helix: -3.17 (0.78), residues: 26 sheet: -0.21 (0.48), residues: 125 loop : -1.48 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 61 TYR 0.022 0.002 TYR A 495 PHE 0.024 0.002 PHE A 338 TRP 0.008 0.002 TRP M 35 HIS 0.003 0.001 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 ( 3453) covalent geometry : angle 0.72450 / 0.37 ( 4687) SS BOND : bond 0.00682 / 0.36 ( 5) SS BOND : angle 3.69569 / 1.98 ( 10) hydrogen bonds : bond 0.04545 / 3.10 ( 71) hydrogen bonds : angle 6.55786 / 4.59 ( 186) link_BETA1-4 : bond 0.00705 / 0.37 ( 1) link_BETA1-4 : angle 2.54994 / 1.33 ( 3) link_NAG-ASN : bond 0.00823 / 0.43 ( 2) link_NAG-ASN : angle 4.33044 / 2.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 517 LEU cc_start: 0.7025 (mm) cc_final: 0.6567 (pp) outliers start: 2 outliers final: 0 residues processed: 72 average time/residue: 0.0464 time to fit residues: 4.2759 Evaluate side-chains 45 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.0020 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.0670 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.5326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN I 32 ASN I 76 ASN I 83 ASN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.087935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077024 restraints weight = 13876.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.078562 restraints weight = 9479.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.079743 restraints weight = 7191.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.080601 restraints weight = 5813.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.081236 restraints weight = 4920.065| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3461 Z= 0.113 Angle : 0.643 7.882 4706 Z= 0.319 Chirality : 0.046 0.184 509 Planarity : 0.004 0.040 601 Dihedral : 7.910 56.825 532 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.27 % Allowed : 3.01 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.39), residues: 418 helix: -3.10 (0.79), residues: 25 sheet: -0.20 (0.48), residues: 127 loop : -1.35 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 86 TYR 0.012 0.001 TYR M 49 PHE 0.011 0.001 PHE M 71 TRP 0.008 0.001 TRP A 452 HIS 0.001 0.000 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 3453) covalent geometry : angle 0.62382 / 0.31 ( 4687) SS BOND : bond 0.00603 / 0.33 ( 5) SS BOND : angle 1.59211 / 0.80 ( 10) hydrogen bonds : bond 0.03496 / 2.36 ( 71) hydrogen bonds : angle 5.86952 / 4.09 ( 186) link_BETA1-4 : bond 0.00735 / 0.39 ( 1) link_BETA1-4 : angle 3.31003 / 1.74 ( 3) link_NAG-ASN : bond 0.00264 / 0.14 ( 2) link_NAG-ASN : angle 3.21040 / 1.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: M 11 LEU cc_start: 0.8156 (mt) cc_final: 0.7926 (mp) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.0408 time to fit residues: 3.6093 Evaluate side-chains 54 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.087323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.076571 restraints weight = 13809.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.078193 restraints weight = 9344.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.079371 restraints weight = 6991.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.080205 restraints weight = 5617.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.080699 restraints weight = 4755.865| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3461 Z= 0.128 Angle : 0.640 8.253 4706 Z= 0.318 Chirality : 0.046 0.186 509 Planarity : 0.004 0.041 601 Dihedral : 7.438 51.528 532 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.39), residues: 418 helix: -2.98 (0.86), residues: 26 sheet: -0.18 (0.49), residues: 127 loop : -1.37 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 66 TYR 0.012 0.001 TYR A 495 PHE 0.024 0.002 PHE A 342 TRP 0.006 0.001 TRP M 35 HIS 0.002 0.001 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 3453) covalent geometry : angle 0.62096 / 0.31 ( 4687) SS BOND : bond 0.00520 / 0.29 ( 5) SS BOND : angle 1.40988 / 0.76 ( 10) hydrogen bonds : bond 0.03523 / 2.34 ( 71) hydrogen bonds : angle 5.69577 / 3.92 ( 186) link_BETA1-4 : bond 0.00496 / 0.26 ( 1) link_BETA1-4 : angle 3.22765 / 1.70 ( 3) link_NAG-ASN : bond 0.00505 / 0.26 ( 2) link_NAG-ASN : angle 3.38914 / 1.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.072 Fit side-chains REVERT: M 11 LEU cc_start: 0.8189 (mt) cc_final: 0.7909 (mp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0444 time to fit residues: 3.7548 Evaluate side-chains 51 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.0270 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.087611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.076735 restraints weight = 14086.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.078340 restraints weight = 9577.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.079534 restraints weight = 7229.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.080387 restraints weight = 5820.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.080950 restraints weight = 4932.558| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3461 Z= 0.117 Angle : 0.632 8.826 4706 Z= 0.315 Chirality : 0.046 0.201 509 Planarity : 0.004 0.041 601 Dihedral : 6.971 43.157 532 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.39), residues: 418 helix: -2.92 (0.99), residues: 20 sheet: -0.19 (0.50), residues: 122 loop : -1.28 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 86 TYR 0.010 0.001 TYR M 49 PHE 0.013 0.001 PHE M 71 TRP 0.006 0.001 TRP A 452 HIS 0.001 0.000 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 3453) covalent geometry : angle 0.61374 / 0.31 ( 4687) SS BOND : bond 0.00558 / 0.30 ( 5) SS BOND : angle 1.43884 / 0.77 ( 10) hydrogen bonds : bond 0.03256 / 2.19 ( 71) hydrogen bonds : angle 5.60063 / 3.86 ( 186) link_BETA1-4 : bond 0.00469 / 0.25 ( 1) link_BETA1-4 : angle 3.25210 / 1.71 ( 3) link_NAG-ASN : bond 0.00261 / 0.14 ( 2) link_NAG-ASN : angle 3.18990 / 1.71 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.075 Fit side-chains REVERT: M 11 LEU cc_start: 0.8163 (mt) cc_final: 0.7861 (mp) REVERT: M 33 LEU cc_start: 0.8716 (tt) cc_final: 0.8123 (mm) REVERT: M 70 GLU cc_start: 0.7790 (pm20) cc_final: 0.7568 (pm20) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0413 time to fit residues: 3.4119 Evaluate side-chains 48 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.087432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.076616 restraints weight = 14386.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.078235 restraints weight = 9646.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.079408 restraints weight = 7243.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.080282 restraints weight = 5830.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.080817 restraints weight = 4930.187| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3461 Z= 0.122 Angle : 0.644 9.209 4706 Z= 0.317 Chirality : 0.048 0.273 509 Planarity : 0.004 0.042 601 Dihedral : 6.699 40.169 532 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.39), residues: 418 helix: -3.10 (0.80), residues: 26 sheet: -0.11 (0.50), residues: 123 loop : -1.34 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 86 TYR 0.010 0.001 TYR A 495 PHE 0.014 0.002 PHE M 71 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 3453) covalent geometry : angle 0.62662 / 0.31 ( 4687) SS BOND : bond 0.00568 / 0.30 ( 5) SS BOND : angle 1.42768 / 0.77 ( 10) hydrogen bonds : bond 0.03272 / 2.22 ( 71) hydrogen bonds : angle 5.37149 / 3.69 ( 186) link_BETA1-4 : bond 0.00238 / 0.13 ( 1) link_BETA1-4 : angle 3.25307 / 1.72 ( 3) link_NAG-ASN : bond 0.00227 / 0.12 ( 2) link_NAG-ASN : angle 3.09759 / 1.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 11 LEU cc_start: 0.8152 (mt) cc_final: 0.7854 (mp) REVERT: M 33 LEU cc_start: 0.8745 (tt) cc_final: 0.8199 (mm) REVERT: M 70 GLU cc_start: 0.7842 (pm20) cc_final: 0.7597 (pm20) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0416 time to fit residues: 3.5202 Evaluate side-chains 51 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.0370 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.087165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.076319 restraints weight = 14063.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.077975 restraints weight = 9456.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.079167 restraints weight = 7064.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.080035 restraints weight = 5671.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.080636 restraints weight = 4806.060| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3461 Z= 0.118 Angle : 0.630 9.682 4706 Z= 0.313 Chirality : 0.047 0.253 509 Planarity : 0.004 0.041 601 Dihedral : 6.608 38.126 532 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.39), residues: 418 helix: -2.94 (0.85), residues: 25 sheet: 0.04 (0.51), residues: 118 loop : -1.41 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 96 TYR 0.009 0.001 TYR M 49 PHE 0.012 0.001 PHE M 71 TRP 0.006 0.001 TRP A 353 HIS 0.001 0.000 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 3453) covalent geometry : angle 0.61263 / 0.31 ( 4687) SS BOND : bond 0.00595 / 0.31 ( 5) SS BOND : angle 1.69363 / 0.88 ( 10) hydrogen bonds : bond 0.03135 / 2.04 ( 71) hydrogen bonds : angle 5.40742 / 3.70 ( 186) link_BETA1-4 : bond 0.00274 / 0.14 ( 1) link_BETA1-4 : angle 3.10841 / 1.65 ( 3) link_NAG-ASN : bond 0.00187 / 0.10 ( 2) link_NAG-ASN : angle 2.88965 / 1.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: M 11 LEU cc_start: 0.8071 (mt) cc_final: 0.7824 (mp) REVERT: M 33 LEU cc_start: 0.8735 (tt) cc_final: 0.8219 (mm) REVERT: M 70 GLU cc_start: 0.7812 (pm20) cc_final: 0.7578 (pm20) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0510 time to fit residues: 4.4147 Evaluate side-chains 51 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 20 optimal weight: 0.1980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.087820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.077132 restraints weight = 14068.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.078765 restraints weight = 9447.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.079932 restraints weight = 7073.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.080668 restraints weight = 5675.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.081311 restraints weight = 4857.502| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3461 Z= 0.112 Angle : 0.633 9.038 4706 Z= 0.315 Chirality : 0.047 0.238 509 Planarity : 0.004 0.042 601 Dihedral : 6.311 35.115 532 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.39), residues: 418 helix: -2.95 (0.82), residues: 26 sheet: 0.14 (0.51), residues: 118 loop : -1.38 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 96 TYR 0.010 0.001 TYR A 351 PHE 0.012 0.001 PHE M 71 TRP 0.005 0.001 TRP A 452 HIS 0.001 0.000 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 3453) covalent geometry : angle 0.61849 / 0.31 ( 4687) SS BOND : bond 0.00457 / 0.25 ( 5) SS BOND : angle 1.45483 / 0.79 ( 10) hydrogen bonds : bond 0.03080 / 2.04 ( 71) hydrogen bonds : angle 5.24387 / 3.58 ( 186) link_BETA1-4 : bond 0.00216 / 0.11 ( 1) link_BETA1-4 : angle 3.03855 / 1.62 ( 3) link_NAG-ASN : bond 0.00131 / 0.07 ( 2) link_NAG-ASN : angle 2.79031 / 1.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 11 LEU cc_start: 0.8073 (mt) cc_final: 0.7831 (mp) REVERT: M 33 LEU cc_start: 0.8713 (tt) cc_final: 0.8209 (mm) REVERT: M 70 GLU cc_start: 0.7858 (pm20) cc_final: 0.7613 (pm20) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0647 time to fit residues: 5.4970 Evaluate side-chains 52 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.0470 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 19 optimal weight: 0.0270 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.088307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.077501 restraints weight = 14427.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.079220 restraints weight = 9708.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.080427 restraints weight = 7261.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.081184 restraints weight = 5842.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.081829 restraints weight = 4999.534| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3461 Z= 0.106 Angle : 0.622 10.244 4706 Z= 0.307 Chirality : 0.047 0.229 509 Planarity : 0.004 0.042 601 Dihedral : 6.012 32.341 532 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.39), residues: 418 helix: -3.12 (0.87), residues: 26 sheet: 0.08 (0.50), residues: 118 loop : -1.38 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 96 TYR 0.010 0.001 TYR A 351 PHE 0.024 0.002 PHE A 342 TRP 0.005 0.001 TRP A 452 HIS 0.001 0.000 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 3453) covalent geometry : angle 0.60721 / 0.30 ( 4687) SS BOND : bond 0.00343 / 0.19 ( 5) SS BOND : angle 1.55111 / 0.86 ( 10) hydrogen bonds : bond 0.02964 / 1.94 ( 71) hydrogen bonds : angle 5.31732 / 3.56 ( 186) link_BETA1-4 : bond 0.00214 / 0.11 ( 1) link_BETA1-4 : angle 3.08646 / 1.64 ( 3) link_NAG-ASN : bond 0.00282 / 0.15 ( 2) link_NAG-ASN : angle 2.64039 / 1.40 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 11 LEU cc_start: 0.8050 (mt) cc_final: 0.7779 (mp) REVERT: M 33 LEU cc_start: 0.8685 (tt) cc_final: 0.8229 (mm) REVERT: M 70 GLU cc_start: 0.7827 (pm20) cc_final: 0.7592 (pm20) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0633 time to fit residues: 5.4915 Evaluate side-chains 54 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.0670 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 0.0040 chunk 23 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 overall best weight: 0.6734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.087918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.077070 restraints weight = 14335.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.078699 restraints weight = 9641.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.079875 restraints weight = 7244.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.080722 restraints weight = 5870.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.081317 restraints weight = 4987.633| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3461 Z= 0.112 Angle : 0.624 10.025 4706 Z= 0.306 Chirality : 0.047 0.236 509 Planarity : 0.004 0.042 601 Dihedral : 6.077 32.867 532 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.39), residues: 418 helix: -3.00 (0.80), residues: 26 sheet: -0.03 (0.50), residues: 119 loop : -1.36 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 86 TYR 0.010 0.001 TYR A 351 PHE 0.012 0.001 PHE M 71 TRP 0.005 0.001 TRP A 353 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 3453) covalent geometry : angle 0.60889 / 0.30 ( 4687) SS BOND : bond 0.00481 / 0.25 ( 5) SS BOND : angle 1.62515 / 0.85 ( 10) hydrogen bonds : bond 0.03010 / 1.97 ( 71) hydrogen bonds : angle 5.26398 / 3.55 ( 186) link_BETA1-4 : bond 0.00218 / 0.11 ( 1) link_BETA1-4 : angle 2.84734 / 1.52 ( 3) link_NAG-ASN : bond 0.00197 / 0.10 ( 2) link_NAG-ASN : angle 2.67431 / 1.42 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 639.53 seconds wall clock time: 11 minutes 42.40 seconds (702.40 seconds total)