Starting phenix.real_space_refine on Wed Jul 1 22:21:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yh6_33820/07_2026/7yh6_33820.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yh6_33820/07_2026/7yh6_33820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7yh6_33820/07_2026/7yh6_33820.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yh6_33820/07_2026/7yh6_33820.cif" model { file = "/net/cci-nas-00/data/ceres_data/7yh6_33820/07_2026/7yh6_33820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yh6_33820/07_2026/7yh6_33820.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yh6_33820/07_2026/7yh6_33820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yh6_33820/07_2026/7yh6_33820.map" } resolution = 3.4 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= 0.001 sd= 0.008 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 14 5.16 5 C 2121 2.51 5 N 563 2.21 5 O 645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3343 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 823 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "H" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} 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 chiralities: 1 Time building chain proxies: 0.75, per 1000 atoms: 0.22 Number of scatterers: 3343 At special positions: 0 Unit cell: (58.29, 75.04, 97.82, 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 14 16.00 O 645 8.00 N 563 7.00 C 2121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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 NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.16 Conformation dependent library (CDL) restraints added in 133.8 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 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: 9 helices and 8 sheets defined 11.9% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'L' and resid 81 through 85 removed outlier: 4.081A pdb=" N ASP L 84 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU L 85 " --> pdb=" O THR L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.281A pdb=" N THR H 91 " --> pdb=" O PRO H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.657A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.504A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.213A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.569A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.805A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.688A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 10 removed outlier: 4.052A pdb=" N ALA L 86 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 9 through 10 removed outlier: 4.052A pdb=" N ALA L 86 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU L 99 " --> pdb=" O ASP L 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.656A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.739A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.517A pdb=" N PHE H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.624A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 102 hydrogen bonds defined for protein. 252 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: 0.47 Time building geometry restraints manager: 0.22 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: 1082 1.34 - 1.46: 917 1.46 - 1.58: 1416 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3431 Sorted by residual: bond pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " ideal model delta sigma weight residual 1.534 1.515 0.019 1.77e-02 3.19e+03 1.18e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.427 -0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.10e+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 9.95e-01 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.469 0.029 3.10e-02 1.04e+03 8.84e-01 ... (remaining 3426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 4602 2.27 - 4.55: 58 4.55 - 6.82: 4 6.82 - 9.09: 1 9.09 - 11.37: 2 Bond angle restraints: 4667 Sorted by residual: angle pdb=" N VAL A 524 " pdb=" CA VAL A 524 " pdb=" C VAL A 524 " ideal model delta sigma weight residual 106.42 113.30 -6.88 1.51e+00 4.39e-01 2.07e+01 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 124.22 -9.82 2.30e+00 1.89e-01 1.82e+01 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 109.14 114.72 -5.58 1.49e+00 4.50e-01 1.40e+01 angle pdb=" C THR A 523 " pdb=" N VAL A 524 " pdb=" CA VAL A 524 " ideal model delta sigma weight residual 122.96 120.03 2.93 9.50e-01 1.11e+00 9.50e+00 angle pdb=" N VAL A 524 " pdb=" CA VAL A 524 " pdb=" CB VAL A 524 " ideal model delta sigma weight residual 112.65 109.98 2.67 1.00e+00 1.00e+00 7.12e+00 ... (remaining 4662 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 1792 17.61 - 35.22: 173 35.22 - 52.83: 23 52.83 - 70.44: 5 70.44 - 88.05: 3 Dihedral angle restraints: 1996 sinusoidal: 764 harmonic: 1232 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 2.05 -88.05 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+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 -121.23 35.23 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 1993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 352 0.046 - 0.092: 103 0.092 - 0.138: 40 0.138 - 0.184: 0 0.184 - 0.230: 2 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA CYS A 391 " pdb=" N CYS A 391 " pdb=" C CYS A 391 " pdb=" CB CYS A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB THR A 430 " pdb=" CA THR A 430 " pdb=" OG1 THR A 430 " pdb=" CG2 THR A 430 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE L 20 " pdb=" N ILE L 20 " pdb=" C ILE L 20 " pdb=" CB ILE L 20 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 494 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 60 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO L 61 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.012 2.00e-02 2.50e+03 1.11e-02 1.54e+00 pdb=" CG ASN A 343 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.011 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 347 " 0.010 2.00e-02 2.50e+03 8.56e-03 1.28e+00 pdb=" CG PHE A 347 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A 347 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 347 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 347 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 347 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 347 " 0.001 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 128 2.71 - 3.26: 3160 3.26 - 3.80: 4834 3.80 - 4.35: 5934 4.35 - 4.90: 10656 Nonbonded interactions: 24712 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" OE2 GLU A 516 " model vdw 2.161 3.040 nonbonded pdb=" O PHE H 29 " pdb=" NH2 ARG H 72 " model vdw 2.237 3.120 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.257 3.040 nonbonded pdb=" OG SER H 17 " pdb=" O MET H 83 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.280 3.040 ... (remaining 24707 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.020 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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 0.029 3438 Z= 0.202 Angle : 0.657 11.365 4682 Z= 0.332 Chirality : 0.048 0.230 497 Planarity : 0.004 0.036 611 Dihedral : 13.140 80.334 1202 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.08 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.42), residues: 424 helix: -3.28 (0.65), residues: 33 sheet: 0.96 (0.47), residues: 141 loop : -1.15 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 72 TYR 0.010 0.001 TYR H 106 PHE 0.019 0.001 PHE A 347 TRP 0.014 0.002 TRP H 36 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 ( 3431) covalent geometry : angle 0.63506 / 0.32 ( 4667) SS BOND : bond 0.00478 / 0.23 ( 6) SS BOND : angle 2.97969 / 1.80 ( 12) hydrogen bonds : bond 0.26985 / 17.63 ( 93) hydrogen bonds : angle 9.47683 / 7.04 ( 252) link_NAG-ASN : bond 0.00272 / 0.14 ( 1) link_NAG-ASN : angle 3.23820 / 1.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: H 56 ASN cc_start: 0.9234 (m110) cc_final: 0.8833 (m110) REVERT: H 62 ASP cc_start: 0.8516 (t70) cc_final: 0.8302 (t0) REVERT: H 73 ASP cc_start: 0.8079 (t0) cc_final: 0.7637 (t0) REVERT: H 99 ASP cc_start: 0.8765 (t70) cc_final: 0.8530 (t0) REVERT: A 420 ASP cc_start: 0.8704 (m-30) cc_final: 0.8301 (m-30) REVERT: A 489 TYR cc_start: 0.8761 (m-10) cc_final: 0.8525 (m-10) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0600 time to fit residues: 4.9827 Evaluate side-chains 60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.077361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.056752 restraints weight = 8266.933| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 3.82 r_work: 0.2583 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3438 Z= 0.136 Angle : 0.631 10.319 4682 Z= 0.320 Chirality : 0.046 0.147 497 Planarity : 0.004 0.039 611 Dihedral : 4.154 17.087 475 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.48 % Favored : 95.05 % Rotamer: Outliers : 0.83 % Allowed : 9.17 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.41), residues: 424 helix: -3.34 (0.62), residues: 33 sheet: 0.86 (0.45), residues: 144 loop : -1.10 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 17 TYR 0.018 0.001 TYR H 53 PHE 0.010 0.001 PHE A 347 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 3431) covalent geometry : angle 0.61883 / 0.32 ( 4667) SS BOND : bond 0.00436 / 0.22 ( 6) SS BOND : angle 2.44931 / 1.46 ( 12) hydrogen bonds : bond 0.04911 / 3.35 ( 93) hydrogen bonds : angle 6.61955 / 4.89 ( 252) link_NAG-ASN : bond 0.00208 / 0.11 ( 1) link_NAG-ASN : angle 1.44753 / 0.84 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.193 Fit side-chains REVERT: L 85 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7424 (pm20) REVERT: H 43 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8168 (mmmt) REVERT: H 56 ASN cc_start: 0.9289 (m110) cc_final: 0.8915 (m110) REVERT: H 73 ASP cc_start: 0.8297 (t0) cc_final: 0.7863 (t0) REVERT: A 420 ASP cc_start: 0.9063 (m-30) cc_final: 0.8662 (m-30) REVERT: A 525 CYS cc_start: 0.6528 (p) cc_final: 0.6300 (p) outliers start: 3 outliers final: 3 residues processed: 67 average time/residue: 0.0622 time to fit residues: 5.2337 Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 117 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.057617 restraints weight = 8186.525| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.87 r_work: 0.2590 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3438 Z= 0.117 Angle : 0.579 9.219 4682 Z= 0.294 Chirality : 0.045 0.132 497 Planarity : 0.004 0.042 611 Dihedral : 3.952 12.777 475 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.42 % Favored : 94.34 % Rotamer: Outliers : 1.67 % Allowed : 11.94 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.41), residues: 424 helix: -3.16 (0.68), residues: 33 sheet: 0.80 (0.44), residues: 152 loop : -1.13 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 44 TYR 0.018 0.001 TYR H 53 PHE 0.008 0.001 PHE L 51 TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 3431) covalent geometry : angle 0.56835 / 0.29 ( 4667) SS BOND : bond 0.00339 / 0.17 ( 6) SS BOND : angle 2.17207 / 1.30 ( 12) hydrogen bonds : bond 0.04077 / 2.83 ( 93) hydrogen bonds : angle 6.08139 / 4.47 ( 252) link_NAG-ASN : bond 0.00126 / 0.07 ( 1) link_NAG-ASN : angle 1.04286 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.076 Fit side-chains REVERT: L 85 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7425 (pm20) REVERT: H 43 LYS cc_start: 0.8224 (mmmt) cc_final: 0.7968 (mmmt) REVERT: H 56 ASN cc_start: 0.9299 (m110) cc_final: 0.8904 (m110) REVERT: H 73 ASP cc_start: 0.7980 (t0) cc_final: 0.7542 (t0) REVERT: A 420 ASP cc_start: 0.9065 (m-30) cc_final: 0.8615 (m-30) outliers start: 6 outliers final: 5 residues processed: 67 average time/residue: 0.0427 time to fit residues: 3.5548 Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.077062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.056409 restraints weight = 8233.984| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 3.75 r_work: 0.2568 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3438 Z= 0.186 Angle : 0.616 8.685 4682 Z= 0.314 Chirality : 0.046 0.135 497 Planarity : 0.004 0.041 611 Dihedral : 4.078 14.732 475 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.13 % Favored : 93.63 % Rotamer: Outliers : 1.94 % Allowed : 13.61 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.41), residues: 424 helix: -2.95 (0.72), residues: 33 sheet: 0.69 (0.44), residues: 152 loop : -1.17 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.019 0.001 TYR H 53 PHE 0.009 0.001 PHE A 347 TRP 0.008 0.001 TRP A 436 HIS 0.006 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 3431) covalent geometry : angle 0.60488 / 0.31 ( 4667) SS BOND : bond 0.00445 / 0.23 ( 6) SS BOND : angle 2.31627 / 1.38 ( 12) hydrogen bonds : bond 0.04360 / 3.08 ( 93) hydrogen bonds : angle 5.97444 / 4.41 ( 252) link_NAG-ASN : bond 0.00070 / 0.04 ( 1) link_NAG-ASN : angle 0.96038 / 0.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.135 Fit side-chains REVERT: L 16 GLN cc_start: 0.8507 (pm20) cc_final: 0.8254 (pm20) REVERT: L 85 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7517 (pm20) REVERT: H 43 LYS cc_start: 0.8257 (mmmt) cc_final: 0.8017 (mmmt) REVERT: H 56 ASN cc_start: 0.9293 (m110) cc_final: 0.8903 (m110) REVERT: H 73 ASP cc_start: 0.8038 (t0) cc_final: 0.7600 (t0) REVERT: A 420 ASP cc_start: 0.9065 (m-30) cc_final: 0.8579 (m-30) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 0.0459 time to fit residues: 3.7742 Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.074736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.054497 restraints weight = 8144.850| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 3.67 r_work: 0.2531 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3438 Z= 0.271 Angle : 0.666 8.876 4682 Z= 0.342 Chirality : 0.047 0.138 497 Planarity : 0.004 0.042 611 Dihedral : 4.394 16.531 475 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.50 % Allowed : 15.56 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.41), residues: 424 helix: -2.89 (0.75), residues: 33 sheet: 0.59 (0.44), residues: 152 loop : -1.24 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.019 0.002 TYR H 53 PHE 0.010 0.001 PHE A 347 TRP 0.008 0.002 TRP A 436 HIS 0.007 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.27 ( 3431) covalent geometry : angle 0.65387 / 0.34 ( 4667) SS BOND : bond 0.00529 / 0.25 ( 6) SS BOND : angle 2.50636 / 1.49 ( 12) hydrogen bonds : bond 0.04872 / 3.48 ( 93) hydrogen bonds : angle 6.05915 / 4.49 ( 252) link_NAG-ASN : bond 0.00028 / 0.01 ( 1) link_NAG-ASN : angle 1.09029 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.076 Fit side-chains REVERT: L 44 ARG cc_start: 0.7879 (mmm160) cc_final: 0.7677 (mmm160) REVERT: L 85 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7668 (pm20) REVERT: H 43 LYS cc_start: 0.8341 (mmmt) cc_final: 0.8109 (mmmt) REVERT: H 56 ASN cc_start: 0.9304 (m110) cc_final: 0.8860 (m110) REVERT: H 73 ASP cc_start: 0.8068 (t0) cc_final: 0.7690 (t0) REVERT: A 420 ASP cc_start: 0.9075 (m-30) cc_final: 0.8567 (m-30) outliers start: 9 outliers final: 4 residues processed: 67 average time/residue: 0.0510 time to fit residues: 4.3061 Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.057092 restraints weight = 8175.187| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.82 r_work: 0.2579 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3438 Z= 0.122 Angle : 0.581 7.536 4682 Z= 0.298 Chirality : 0.045 0.157 497 Planarity : 0.004 0.041 611 Dihedral : 4.080 13.425 475 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.11 % Allowed : 17.22 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.41), residues: 424 helix: -2.97 (0.73), residues: 33 sheet: 0.61 (0.44), residues: 153 loop : -1.19 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 16 TYR 0.018 0.001 TYR H 53 PHE 0.010 0.001 PHE L 51 TRP 0.009 0.001 TRP H 47 HIS 0.007 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3431) covalent geometry : angle 0.57070 / 0.29 ( 4667) SS BOND : bond 0.00433 / 0.26 ( 6) SS BOND : angle 2.24037 / 1.35 ( 12) hydrogen bonds : bond 0.03695 / 2.61 ( 93) hydrogen bonds : angle 5.74067 / 4.21 ( 252) link_NAG-ASN : bond 0.00164 / 0.09 ( 1) link_NAG-ASN : angle 0.84782 / 0.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.131 Fit side-chains REVERT: L 85 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7568 (pm20) REVERT: H 43 LYS cc_start: 0.8132 (mmmt) cc_final: 0.7908 (mmmt) REVERT: H 56 ASN cc_start: 0.9325 (m110) cc_final: 0.8917 (m110) REVERT: H 73 ASP cc_start: 0.7839 (t0) cc_final: 0.7423 (t0) REVERT: A 420 ASP cc_start: 0.9048 (m-30) cc_final: 0.8530 (m-30) outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.0416 time to fit residues: 3.7552 Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.0040 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.076420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.056089 restraints weight = 8528.617| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.77 r_work: 0.2566 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3438 Z= 0.167 Angle : 0.625 8.281 4682 Z= 0.318 Chirality : 0.046 0.154 497 Planarity : 0.004 0.041 611 Dihedral : 4.101 14.683 475 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.11 % Allowed : 17.50 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.41), residues: 424 helix: -2.97 (0.73), residues: 33 sheet: 0.60 (0.44), residues: 152 loop : -1.18 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.017 0.001 TYR H 53 PHE 0.010 0.001 PHE L 51 TRP 0.007 0.001 TRP A 436 HIS 0.007 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 3431) covalent geometry : angle 0.61173 / 0.31 ( 4667) SS BOND : bond 0.00449 / 0.22 ( 6) SS BOND : angle 2.54985 / 1.69 ( 12) hydrogen bonds : bond 0.04038 / 2.90 ( 93) hydrogen bonds : angle 5.74628 / 4.24 ( 252) link_NAG-ASN : bond 0.00089 / 0.05 ( 1) link_NAG-ASN : angle 0.88561 / 0.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.128 Fit side-chains REVERT: L 85 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7741 (pm20) REVERT: H 43 LYS cc_start: 0.8221 (mmmt) cc_final: 0.8007 (mmmt) REVERT: H 56 ASN cc_start: 0.9301 (m110) cc_final: 0.8871 (m110) REVERT: H 73 ASP cc_start: 0.8012 (t0) cc_final: 0.7598 (t0) REVERT: A 420 ASP cc_start: 0.9074 (m-30) cc_final: 0.8566 (m-30) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 0.0492 time to fit residues: 3.9354 Evaluate side-chains 63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.0040 chunk 15 optimal weight: 0.0370 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.4870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.057844 restraints weight = 8373.140| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.90 r_work: 0.2596 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3438 Z= 0.103 Angle : 0.591 7.897 4682 Z= 0.300 Chirality : 0.044 0.131 497 Planarity : 0.004 0.041 611 Dihedral : 3.881 12.351 475 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.83 % Allowed : 17.78 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.41), residues: 424 helix: -2.99 (0.72), residues: 33 sheet: 0.65 (0.44), residues: 152 loop : -1.12 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 44 TYR 0.016 0.001 TYR H 53 PHE 0.010 0.001 PHE L 51 TRP 0.007 0.001 TRP H 47 HIS 0.007 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 3431) covalent geometry : angle 0.58053 / 0.30 ( 4667) SS BOND : bond 0.00347 / 0.18 ( 6) SS BOND : angle 2.21496 / 1.38 ( 12) hydrogen bonds : bond 0.03369 / 2.41 ( 93) hydrogen bonds : angle 5.54454 / 4.07 ( 252) link_NAG-ASN : bond 0.00167 / 0.09 ( 1) link_NAG-ASN : angle 0.79799 / 0.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.121 Fit side-chains REVERT: L 85 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7615 (pm20) REVERT: H 43 LYS cc_start: 0.8084 (mmmt) cc_final: 0.7875 (mmmt) REVERT: H 56 ASN cc_start: 0.9320 (m110) cc_final: 0.8907 (m110) REVERT: H 73 ASP cc_start: 0.7907 (t0) cc_final: 0.7538 (t0) REVERT: A 420 ASP cc_start: 0.9062 (m-30) cc_final: 0.8543 (m-30) outliers start: 3 outliers final: 2 residues processed: 68 average time/residue: 0.0605 time to fit residues: 5.0268 Evaluate side-chains 66 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.077092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.056635 restraints weight = 8402.381| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.86 r_work: 0.2568 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3438 Z= 0.158 Angle : 0.626 8.088 4682 Z= 0.316 Chirality : 0.045 0.133 497 Planarity : 0.004 0.040 611 Dihedral : 3.997 13.673 475 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.39 % Allowed : 18.33 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.41), residues: 424 helix: -3.00 (0.72), residues: 33 sheet: 0.67 (0.44), residues: 152 loop : -1.12 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 19 TYR 0.021 0.001 TYR H 80 PHE 0.010 0.001 PHE L 51 TRP 0.008 0.001 TRP A 436 HIS 0.007 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 3431) covalent geometry : angle 0.61671 / 0.31 ( 4667) SS BOND : bond 0.00413 / 0.20 ( 6) SS BOND : angle 2.21702 / 1.37 ( 12) hydrogen bonds : bond 0.03848 / 2.78 ( 93) hydrogen bonds : angle 5.62345 / 4.16 ( 252) link_NAG-ASN : bond 0.00092 / 0.05 ( 1) link_NAG-ASN : angle 0.87031 / 0.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.125 Fit side-chains REVERT: L 85 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7617 (pm20) REVERT: H 56 ASN cc_start: 0.9318 (m110) cc_final: 0.8879 (m110) REVERT: H 73 ASP cc_start: 0.7905 (t0) cc_final: 0.7523 (t0) REVERT: A 355 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.7632 (ttm-80) REVERT: A 420 ASP cc_start: 0.9063 (m-30) cc_final: 0.8540 (m-30) outliers start: 5 outliers final: 2 residues processed: 67 average time/residue: 0.0575 time to fit residues: 4.7576 Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.057248 restraints weight = 8302.749| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.84 r_work: 0.2584 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3438 Z= 0.132 Angle : 0.665 10.072 4682 Z= 0.333 Chirality : 0.045 0.132 497 Planarity : 0.004 0.039 611 Dihedral : 3.975 12.765 475 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.56 % Allowed : 18.89 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.41), residues: 424 helix: -2.98 (0.72), residues: 33 sheet: 0.70 (0.44), residues: 152 loop : -1.11 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 16 TYR 0.019 0.001 TYR H 80 PHE 0.010 0.001 PHE L 51 TRP 0.007 0.001 TRP A 436 HIS 0.007 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 3431) covalent geometry : angle 0.65683 / 0.33 ( 4667) SS BOND : bond 0.00410 / 0.20 ( 6) SS BOND : angle 2.11864 / 1.30 ( 12) hydrogen bonds : bond 0.03608 / 2.61 ( 93) hydrogen bonds : angle 5.55451 / 4.11 ( 252) link_NAG-ASN : bond 0.00126 / 0.07 ( 1) link_NAG-ASN : angle 0.86643 / 0.50 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.072 Fit side-chains REVERT: L 85 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7618 (pm20) REVERT: H 56 ASN cc_start: 0.9307 (m110) cc_final: 0.8881 (m110) REVERT: H 73 ASP cc_start: 0.7886 (t0) cc_final: 0.7493 (t0) REVERT: A 420 ASP cc_start: 0.9039 (m-30) cc_final: 0.8512 (m-30) outliers start: 2 outliers final: 2 residues processed: 64 average time/residue: 0.0509 time to fit residues: 4.0949 Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 0.0050 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 4 optimal weight: 0.0370 chunk 21 optimal weight: 1.9990 overall best weight: 0.5274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.079027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.058437 restraints weight = 8436.080| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.96 r_work: 0.2609 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3438 Z= 0.110 Angle : 0.656 10.892 4682 Z= 0.324 Chirality : 0.044 0.133 497 Planarity : 0.004 0.040 611 Dihedral : 3.824 13.473 475 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.83 % Allowed : 18.61 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.41), residues: 424 helix: -2.99 (0.72), residues: 33 sheet: 0.77 (0.43), residues: 155 loop : -1.03 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 16 TYR 0.015 0.001 TYR H 53 PHE 0.010 0.001 PHE L 51 TRP 0.007 0.001 TRP H 47 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 3431) covalent geometry : angle 0.64991 / 0.32 ( 4667) SS BOND : bond 0.00329 / 0.17 ( 6) SS BOND : angle 1.93242 / 1.18 ( 12) hydrogen bonds : bond 0.03198 / 2.31 ( 93) hydrogen bonds : angle 5.41208 / 4.00 ( 252) link_NAG-ASN : bond 0.00165 / 0.09 ( 1) link_NAG-ASN : angle 0.77987 / 0.44 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 951.72 seconds wall clock time: 17 minutes 6.25 seconds (1026.25 seconds total)