Starting phenix.real_space_refine on Fri Aug 22 13:41:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yh6_33820/08_2025/7yh6_33820.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yh6_33820/08_2025/7yh6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yh6_33820/08_2025/7yh6_33820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yh6_33820/08_2025/7yh6_33820.map" model { file = "/net/cci-nas-00/data/ceres_data/7yh6_33820/08_2025/7yh6_33820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yh6_33820/08_2025/7yh6_33820.cif" } 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-2.0-5787/lib/python3.9/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.06, per 1000 atoms: 0.32 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: 0.27 Conformation dependent library (CDL) restraints added in 129.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.14 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: 0.42 Time building geometry restraints manager: 0.37 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: 1809 17.61 - 35.22: 175 35.22 - 52.83: 25 52.83 - 70.44: 5 70.44 - 88.05: 3 Dihedral angle restraints: 2017 sinusoidal: 785 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 2014 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: 12.340 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.130 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 13.192 80.334 1223 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 aren 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 covalent geometry : bond 0.00463 ( 3431) covalent geometry : angle 0.63506 ( 4667) SS BOND : bond 0.00478 ( 6) SS BOND : angle 2.97969 ( 12) hydrogen bonds : bond 0.26985 ( 93) hydrogen bonds : angle 9.47683 ( 252) link_NAG-ASN : bond 0.00272 ( 1) link_NAG-ASN : angle 3.23820 ( 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 : 0.133 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: 0.8300 (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: 0.0747 time to fit residues: 6.1645 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 : 0.137 ------------------------------------------------------------------------------- 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: 0.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.077355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.056780 restraints weight = 8259.267| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.80 r_work: 0.2580 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3438 Z= 0.139 Angle : 0.633 10.318 4682 Z= 0.322 Chirality : 0.046 0.149 497 Planarity : 0.004 0.039 611 Dihedral : 4.776 33.806 496 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 aren not related in a simple way. whole: -0.88 (0.41), residues: 424 helix: -3.34 (0.62), residues: 33 sheet: 0.84 (0.45), residues: 144 loop : -1.10 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 44 TYR 0.018 0.001 TYR H 53 PHE 0.009 0.001 PHE A 347 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3431) covalent geometry : angle 0.62014 ( 4667) SS BOND : bond 0.00486 ( 6) SS BOND : angle 2.49035 ( 12) hydrogen bonds : bond 0.04989 ( 93) hydrogen bonds : angle 6.61231 ( 252) link_NAG-ASN : bond 0.00120 ( 1) link_NAG-ASN : angle 1.70353 ( 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 : 0.159 Fit side-chains REVERT: L 85 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7381 (pm20) REVERT: H 43 LYS cc_start: 0.8375 (mmmt) cc_final: 0.8147 (mmmt) REVERT: H 56 ASN cc_start: 0.9291 (m110) cc_final: 0.8909 (m110) REVERT: H 73 ASP cc_start: 0.8190 (t0) cc_final: 0.7748 (t0) REVERT: A 420 ASP cc_start: 0.9060 (m-30) cc_final: 0.8648 (m-30) REVERT: A 489 TYR cc_start: 0.8904 (m-10) cc_final: 0.8702 (m-10) REVERT: A 525 CYS cc_start: 0.6520 (p) cc_final: 0.6283 (p) outliers start: 3 outliers final: 3 residues processed: 67 average time/residue: 0.0683 time to fit residues: 5.6558 Evaluate side-chains 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.097 ------------------------------------------------------------------------------- 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: 0.0000 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3147 r_free = 0.3147 target = 0.077992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.057385 restraints weight = 8183.659| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.84 r_work: 0.2584 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3438 Z= 0.127 Angle : 0.585 9.288 4682 Z= 0.298 Chirality : 0.045 0.132 497 Planarity : 0.004 0.040 611 Dihedral : 4.337 29.516 496 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.91 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 aren not related in a simple way. whole: -0.88 (0.41), residues: 424 helix: -3.13 (0.68), residues: 33 sheet: 0.79 (0.44), residues: 152 loop : -1.16 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.018 0.001 TYR H 53 PHE 0.009 0.001 PHE A 347 TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3431) covalent geometry : angle 0.57391 ( 4667) SS BOND : bond 0.00348 ( 6) SS BOND : angle 2.19834 ( 12) hydrogen bonds : bond 0.04159 ( 93) hydrogen bonds : angle 6.06840 ( 252) link_NAG-ASN : bond 0.00182 ( 1) link_NAG-ASN : angle 1.37299 ( 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 71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.144 Fit side-chains REVERT: L 85 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7425 (pm20) REVERT: H 43 LYS cc_start: 0.8227 (mmmt) cc_final: 0.7968 (mmmt) REVERT: H 56 ASN cc_start: 0.9300 (m110) cc_final: 0.8905 (m110) REVERT: H 73 ASP cc_start: 0.7904 (t0) cc_final: 0.7462 (t0) REVERT: A 420 ASP cc_start: 0.9054 (m-30) cc_final: 0.8588 (m-30) REVERT: A 489 TYR cc_start: 0.8877 (m-10) cc_final: 0.8674 (m-10) outliers start: 6 outliers final: 6 residues processed: 66 average time/residue: 0.0637 time to fit residues: 5.2662 Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3134 r_free = 0.3134 target = 0.077230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.056555 restraints weight = 8245.115| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.87 r_work: 0.2566 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3438 Z= 0.157 Angle : 0.595 8.427 4682 Z= 0.303 Chirality : 0.045 0.132 497 Planarity : 0.004 0.041 611 Dihedral : 4.274 26.754 496 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.90 % Favored : 93.87 % Rotamer: Outliers : 1.94 % Allowed : 14.44 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.41), residues: 424 helix: -2.95 (0.72), residues: 33 sheet: 0.70 (0.44), residues: 152 loop : -1.14 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.018 0.001 TYR H 53 PHE 0.010 0.001 PHE L 51 TRP 0.007 0.001 TRP H 47 HIS 0.006 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3431) covalent geometry : angle 0.58421 ( 4667) SS BOND : bond 0.00398 ( 6) SS BOND : angle 2.18408 ( 12) hydrogen bonds : bond 0.04113 ( 93) hydrogen bonds : angle 5.89936 ( 252) link_NAG-ASN : bond 0.00146 ( 1) link_NAG-ASN : angle 1.30569 ( 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 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.131 Fit side-chains REVERT: L 16 GLN cc_start: 0.8497 (pm20) cc_final: 0.8246 (pm20) REVERT: L 85 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7498 (pm20) REVERT: H 43 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7937 (mmmt) REVERT: H 56 ASN cc_start: 0.9300 (m110) cc_final: 0.8886 (m110) REVERT: H 73 ASP cc_start: 0.7895 (t0) cc_final: 0.7466 (t0) REVERT: A 420 ASP cc_start: 0.9072 (m-30) cc_final: 0.8586 (m-30) outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.0723 time to fit residues: 5.6342 Evaluate side-chains 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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: 1.9990 chunk 17 optimal weight: 8.9990 chunk 1 optimal weight: 0.0060 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.076820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.056505 restraints weight = 8109.875| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 3.70 r_work: 0.2576 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3438 Z= 0.165 Angle : 0.591 8.066 4682 Z= 0.302 Chirality : 0.045 0.131 497 Planarity : 0.004 0.041 611 Dihedral : 4.270 24.914 496 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % 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 aren not related in a simple way. whole: -0.95 (0.41), residues: 424 helix: -2.97 (0.72), residues: 33 sheet: 0.66 (0.44), residues: 152 loop : -1.17 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.018 0.001 TYR H 53 PHE 0.009 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 covalent geometry : bond 0.00389 ( 3431) covalent geometry : angle 0.58056 ( 4667) SS BOND : bond 0.00404 ( 6) SS BOND : angle 2.14652 ( 12) hydrogen bonds : bond 0.04079 ( 93) hydrogen bonds : angle 5.80683 ( 252) link_NAG-ASN : bond 0.00133 ( 1) link_NAG-ASN : angle 1.31059 ( 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 73 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.163 Fit side-chains REVERT: L 16 GLN cc_start: 0.8495 (pm20) cc_final: 0.8283 (pm20) REVERT: L 85 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7613 (pm20) REVERT: H 43 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7993 (mmmt) REVERT: H 56 ASN cc_start: 0.9300 (m110) cc_final: 0.8895 (m110) REVERT: H 73 ASP cc_start: 0.8013 (t0) cc_final: 0.7602 (t0) REVERT: A 420 ASP cc_start: 0.9052 (m-30) cc_final: 0.8558 (m-30) outliers start: 9 outliers final: 5 residues processed: 68 average time/residue: 0.0707 time to fit residues: 5.9468 Evaluate side-chains 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 0.0470 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 17 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 28 optimal weight: 0.0470 chunk 35 optimal weight: 2.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3165 r_free = 0.3165 target = 0.078905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.058458 restraints weight = 8117.719| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.84 r_work: 0.2610 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3438 Z= 0.095 Angle : 0.552 6.969 4682 Z= 0.281 Chirality : 0.044 0.130 497 Planarity : 0.003 0.040 611 Dihedral : 4.050 23.908 496 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.39 % Allowed : 17.50 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.41), residues: 424 helix: -2.98 (0.72), residues: 33 sheet: 0.73 (0.44), residues: 152 loop : -1.11 (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 0.009 0.001 PHE L 51 TRP 0.008 0.001 TRP H 47 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 3431) covalent geometry : angle 0.54286 ( 4667) SS BOND : bond 0.00284 ( 6) SS BOND : angle 2.01276 ( 12) hydrogen bonds : bond 0.03354 ( 93) hydrogen bonds : angle 5.56620 ( 252) link_NAG-ASN : bond 0.00212 ( 1) link_NAG-ASN : angle 1.18575 ( 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: 5 poor density : 66 time to evaluate : 0.133 Fit side-chains REVERT: L 16 GLN cc_start: 0.8434 (pm20) cc_final: 0.8211 (pm20) REVERT: L 85 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7630 (pm20) REVERT: H 43 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7864 (mmmt) REVERT: H 56 ASN cc_start: 0.9307 (m110) cc_final: 0.8890 (m110) REVERT: H 73 ASP cc_start: 0.7810 (t0) cc_final: 0.7441 (t0) REVERT: A 420 ASP cc_start: 0.9047 (m-30) cc_final: 0.8529 (m-30) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.0693 time to fit residues: 5.8188 Evaluate side-chains 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR 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: 5.9990 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3147 r_free = 0.3147 target = 0.077649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.057386 restraints weight = 8357.331| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.77 r_work: 0.2596 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3438 Z= 0.130 Angle : 0.582 7.822 4682 Z= 0.296 Chirality : 0.044 0.130 497 Planarity : 0.004 0.040 611 Dihedral : 4.021 22.779 496 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.67 % Allowed : 17.22 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.41), residues: 424 helix: -3.00 (0.72), residues: 33 sheet: 0.76 (0.44), residues: 152 loop : -1.08 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.020 0.001 TYR H 80 PHE 0.009 0.001 PHE L 51 TRP 0.007 0.001 TRP A 436 HIS 0.006 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3431) covalent geometry : angle 0.57181 ( 4667) SS BOND : bond 0.00400 ( 6) SS BOND : angle 2.17264 ( 12) hydrogen bonds : bond 0.03642 ( 93) hydrogen bonds : angle 5.56884 ( 252) link_NAG-ASN : bond 0.00163 ( 1) link_NAG-ASN : angle 1.14661 ( 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 71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.150 Fit side-chains REVERT: L 16 GLN cc_start: 0.8467 (pm20) cc_final: 0.8238 (pm20) REVERT: L 85 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7698 (pm20) REVERT: H 56 ASN cc_start: 0.9304 (m110) cc_final: 0.8895 (m110) REVERT: H 73 ASP cc_start: 0.8027 (t0) cc_final: 0.7617 (t0) REVERT: A 420 ASP cc_start: 0.9073 (m-30) cc_final: 0.8574 (m-30) outliers start: 6 outliers final: 3 residues processed: 68 average time/residue: 0.0647 time to fit residues: 5.4705 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 : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL 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: 5.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3134 r_free = 0.3134 target = 0.076900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.056689 restraints weight = 8313.227| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.71 r_work: 0.2580 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3438 Z= 0.169 Angle : 0.634 7.846 4682 Z= 0.320 Chirality : 0.045 0.132 497 Planarity : 0.004 0.040 611 Dihedral : 4.119 22.027 496 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.22 % Allowed : 17.22 % 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 aren not related in a simple way. whole: -0.86 (0.41), residues: 424 helix: -2.98 (0.72), residues: 33 sheet: 0.76 (0.44), residues: 152 loop : -1.13 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.018 0.001 TYR H 53 PHE 0.009 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 covalent geometry : bond 0.00399 ( 3431) covalent geometry : angle 0.62414 ( 4667) SS BOND : bond 0.00457 ( 6) SS BOND : angle 2.22006 ( 12) hydrogen bonds : bond 0.03863 ( 93) hydrogen bonds : angle 5.61510 ( 252) link_NAG-ASN : bond 0.00125 ( 1) link_NAG-ASN : angle 1.22550 ( 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 74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.079 Fit side-chains REVERT: L 16 GLN cc_start: 0.8483 (pm20) cc_final: 0.8252 (pm20) REVERT: L 85 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7715 (pm20) REVERT: H 56 ASN cc_start: 0.9303 (m110) cc_final: 0.8884 (m110) REVERT: H 73 ASP cc_start: 0.8009 (t0) cc_final: 0.7617 (t0) REVERT: A 420 ASP cc_start: 0.9056 (m-30) cc_final: 0.8543 (m-30) outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 0.0633 time to fit residues: 5.5556 Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3154 r_free = 0.3154 target = 0.078108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.057671 restraints weight = 8364.479| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.88 r_work: 0.2594 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3438 Z= 0.119 Angle : 0.637 8.667 4682 Z= 0.317 Chirality : 0.045 0.134 497 Planarity : 0.003 0.040 611 Dihedral : 4.049 21.541 496 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.56 % Allowed : 19.17 % 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 aren not related in a simple way. whole: -0.78 (0.41), residues: 424 helix: -2.93 (0.74), residues: 33 sheet: 0.82 (0.44), residues: 152 loop : -1.08 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.017 0.001 TYR H 53 PHE 0.009 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 covalent geometry : bond 0.00277 ( 3431) covalent geometry : angle 0.62755 ( 4667) SS BOND : bond 0.00380 ( 6) SS BOND : angle 2.14122 ( 12) hydrogen bonds : bond 0.03400 ( 93) hydrogen bonds : angle 5.50635 ( 252) link_NAG-ASN : bond 0.00182 ( 1) link_NAG-ASN : angle 1.20628 ( 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 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.119 Fit side-chains REVERT: L 16 GLN cc_start: 0.8475 (pm20) cc_final: 0.8243 (pm20) REVERT: L 85 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7701 (pm20) REVERT: H 56 ASN cc_start: 0.9318 (m110) cc_final: 0.8910 (m110) REVERT: H 73 ASP cc_start: 0.7926 (t0) cc_final: 0.7514 (t0) REVERT: A 420 ASP cc_start: 0.9073 (m-30) cc_final: 0.8552 (m-30) outliers start: 2 outliers final: 2 residues processed: 68 average time/residue: 0.0655 time to fit residues: 5.6430 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 : 0.144 ------------------------------------------------------------------------------- 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 8 optimal weight: 6.9990 chunk 5 optimal weight: 0.1980 chunk 17 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3163 r_free = 0.3163 target = 0.078802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.058255 restraints weight = 8201.650| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.89 r_work: 0.2609 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2015 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= 0.115 Angle : 0.640 10.194 4682 Z= 0.317 Chirality : 0.045 0.132 497 Planarity : 0.004 0.039 611 Dihedral : 3.979 20.907 496 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.83 % Allowed : 18.89 % 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 aren not related in a simple way. whole: -0.72 (0.41), residues: 424 helix: -2.97 (0.73), residues: 33 sheet: 0.92 (0.44), residues: 152 loop : -1.07 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.016 0.001 TYR H 53 PHE 0.009 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 covalent geometry : bond 0.00267 ( 3431) covalent geometry : angle 0.63173 ( 4667) SS BOND : bond 0.00339 ( 6) SS BOND : angle 2.00591 ( 12) hydrogen bonds : bond 0.03276 ( 93) hydrogen bonds : angle 5.52237 ( 252) link_NAG-ASN : bond 0.00185 ( 1) link_NAG-ASN : angle 1.15523 ( 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 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.132 Fit side-chains REVERT: L 16 GLN cc_start: 0.8466 (pm20) cc_final: 0.8229 (pm20) REVERT: L 85 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7706 (pm20) REVERT: H 56 ASN cc_start: 0.9312 (m110) cc_final: 0.8901 (m110) REVERT: H 73 ASP cc_start: 0.7995 (t0) cc_final: 0.7601 (t0) REVERT: A 420 ASP cc_start: 0.9075 (m-30) cc_final: 0.8561 (m-30) outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 0.0614 time to fit residues: 5.1601 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 : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR 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: 2.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3158 r_free = 0.3158 target = 0.078427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.057815 restraints weight = 8375.510| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.93 r_work: 0.2598 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3438 Z= 0.127 Angle : 0.652 10.360 4682 Z= 0.324 Chirality : 0.045 0.162 497 Planarity : 0.003 0.039 611 Dihedral : 3.948 20.037 496 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % 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 aren not related in a simple way. whole: -0.70 (0.41), residues: 424 helix: -2.95 (0.73), residues: 33 sheet: 0.91 (0.44), residues: 152 loop : -1.04 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 403 TYR 0.017 0.001 TYR H 53 PHE 0.009 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 covalent geometry : bond 0.00299 ( 3431) covalent geometry : angle 0.64473 ( 4667) SS BOND : bond 0.00372 ( 6) SS BOND : angle 2.02025 ( 12) hydrogen bonds : bond 0.03338 ( 93) hydrogen bonds : angle 5.46062 ( 252) link_NAG-ASN : bond 0.00170 ( 1) link_NAG-ASN : angle 1.15465 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1121.46 seconds wall clock time: 20 minutes 0.97 seconds (1200.97 seconds total)