Starting phenix.real_space_refine on Fri Dec 27 07:49:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yh6_33820/12_2024/7yh6_33820.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yh6_33820/12_2024/7yh6_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_33820/12_2024/7yh6_33820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yh6_33820/12_2024/7yh6_33820.map" model { file = "/net/cci-nas-00/data/ceres_data/7yh6_33820/12_2024/7yh6_33820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yh6_33820/12_2024/7yh6_33820.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 5.64, per 1000 atoms: 1.69 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: 0.82 Conformation dependent library (CDL) restraints added in 449.4 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: 0.43 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: 0.98 Time building geometry restraints manager: 0.97 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: 7.450 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.210 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.050 ------------------------------------------------------------------------------- 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 3431 Z= 0.298 Angle : 0.635 11.365 4667 Z= 0.324 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.002 TRP H 36 HIS 0.004 0.002 HIS H 35 PHE 0.019 0.001 PHE A 347 TYR 0.010 0.001 TYR H 106 ARG 0.006 0.001 ARG H 72 *********************** 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 : 0.405 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: 0.1777 time to fit residues: 14.6452 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 : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3431 Z= 0.182 Angle : 0.608 10.341 4667 Z= 0.309 Chirality : 0.046 0.145 497 Planarity : 0.004 0.039 611 Dihedral : 4.708 33.407 496 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.25 % Favored : 95.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.41), residues: 424 helix: -3.34 (0.62), residues: 33 sheet: 0.83 (0.45), residues: 144 loop : -1.10 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 PHE 0.009 0.001 PHE A 392 TYR 0.017 0.001 TYR H 53 ARG 0.002 0.000 ARG A 403 *********************** 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 71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.437 Fit side-chains REVERT: L 85 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7255 (pm20) REVERT: H 43 LYS cc_start: 0.8324 (mmmt) cc_final: 0.8092 (mmmt) REVERT: H 56 ASN cc_start: 0.9216 (m110) cc_final: 0.8837 (m110) REVERT: H 62 ASP cc_start: 0.8450 (t70) cc_final: 0.8240 (t0) REVERT: H 73 ASP cc_start: 0.8098 (t0) cc_final: 0.7662 (t0) REVERT: A 420 ASP cc_start: 0.8712 (m-30) cc_final: 0.8236 (m-30) REVERT: A 525 CYS cc_start: 0.5659 (p) cc_final: 0.5456 (p) outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 0.1591 time to fit residues: 13.3245 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 : 0.363 ------------------------------------------------------------------------------- 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 31 optimal weight: 0.0370 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3431 Z= 0.152 Angle : 0.560 9.003 4667 Z= 0.285 Chirality : 0.045 0.133 497 Planarity : 0.004 0.042 611 Dihedral : 4.272 30.138 496 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.95 % Favored : 94.81 % Rotamer: Outliers : 0.83 % Allowed : 12.22 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.41), residues: 424 helix: -3.15 (0.68), residues: 33 sheet: 0.79 (0.44), residues: 154 loop : -1.10 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS A 519 PHE 0.008 0.001 PHE L 51 TYR 0.018 0.001 TYR H 53 ARG 0.001 0.000 ARG L 44 *********************** 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: 3 poor density : 69 time to evaluate : 0.431 Fit side-chains REVERT: L 85 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7315 (pm20) REVERT: H 43 LYS cc_start: 0.8230 (mmmt) cc_final: 0.7981 (mmmt) REVERT: H 56 ASN cc_start: 0.9225 (m110) cc_final: 0.8849 (m110) REVERT: H 62 ASP cc_start: 0.8415 (t70) cc_final: 0.8214 (t0) REVERT: H 73 ASP cc_start: 0.8014 (t0) cc_final: 0.7619 (t0) REVERT: A 420 ASP cc_start: 0.8718 (m-30) cc_final: 0.8223 (m-30) outliers start: 3 outliers final: 3 residues processed: 70 average time/residue: 0.1695 time to fit residues: 14.4076 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 : 0.383 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.0040 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.0040 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5204 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3431 Z= 0.140 Angle : 0.547 8.318 4667 Z= 0.277 Chirality : 0.044 0.131 497 Planarity : 0.004 0.041 611 Dihedral : 4.061 27.791 496 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.25 % Favored : 95.52 % Rotamer: Outliers : 1.94 % Allowed : 12.78 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.41), residues: 424 helix: -2.99 (0.73), residues: 33 sheet: 0.74 (0.44), residues: 154 loop : -1.02 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS A 519 PHE 0.008 0.001 PHE L 51 TYR 0.018 0.001 TYR H 53 ARG 0.002 0.000 ARG A 403 *********************** 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 71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.410 Fit side-chains REVERT: L 85 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7360 (pm20) REVERT: H 43 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7851 (mmmt) REVERT: H 56 ASN cc_start: 0.9228 (m110) cc_final: 0.8851 (m110) REVERT: H 73 ASP cc_start: 0.7975 (t0) cc_final: 0.7561 (t0) REVERT: A 369 TYR cc_start: 0.8842 (t80) cc_final: 0.8632 (t80) REVERT: A 420 ASP cc_start: 0.8704 (m-30) cc_final: 0.8196 (m-30) outliers start: 7 outliers final: 7 residues processed: 67 average time/residue: 0.1491 time to fit residues: 12.4090 Evaluate side-chains 66 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.0170 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3431 Z= 0.145 Angle : 0.536 7.566 4667 Z= 0.274 Chirality : 0.044 0.128 497 Planarity : 0.003 0.042 611 Dihedral : 3.921 25.296 496 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.95 % Favored : 94.81 % Rotamer: Outliers : 1.94 % Allowed : 15.00 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.41), residues: 424 helix: -2.97 (0.74), residues: 33 sheet: 0.78 (0.43), residues: 154 loop : -0.99 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.006 0.001 HIS A 519 PHE 0.008 0.001 PHE L 51 TYR 0.017 0.001 TYR H 53 ARG 0.003 0.000 ARG H 16 *********************** 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 71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.406 Fit side-chains REVERT: L 44 ARG cc_start: 0.7286 (mmm160) cc_final: 0.7042 (mmm-85) REVERT: L 85 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7413 (pm20) REVERT: H 56 ASN cc_start: 0.9230 (m110) cc_final: 0.8835 (m110) REVERT: H 73 ASP cc_start: 0.7993 (t0) cc_final: 0.7572 (t0) REVERT: A 369 TYR cc_start: 0.8839 (t80) cc_final: 0.8586 (t80) REVERT: A 420 ASP cc_start: 0.8713 (m-30) cc_final: 0.8200 (m-30) outliers start: 7 outliers final: 7 residues processed: 67 average time/residue: 0.1560 time to fit residues: 12.9403 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 : 0.416 ------------------------------------------------------------------------------- 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 22 CYS Chi-restraints excluded: chain H residue 119 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.0060 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3431 Z= 0.161 Angle : 0.559 7.047 4667 Z= 0.283 Chirality : 0.044 0.128 497 Planarity : 0.003 0.041 611 Dihedral : 3.877 23.397 496 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.72 % Favored : 95.05 % Rotamer: Outliers : 1.94 % Allowed : 16.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.41), residues: 424 helix: -2.94 (0.74), residues: 33 sheet: 0.83 (0.44), residues: 152 loop : -1.01 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.006 0.001 HIS A 519 PHE 0.008 0.001 PHE L 51 TYR 0.017 0.001 TYR H 53 ARG 0.002 0.000 ARG H 16 *********************** 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 72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.496 Fit side-chains REVERT: L 85 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7476 (pm20) REVERT: H 56 ASN cc_start: 0.9237 (m110) cc_final: 0.8844 (m110) REVERT: H 73 ASP cc_start: 0.8019 (t0) cc_final: 0.7592 (t0) REVERT: A 369 TYR cc_start: 0.8836 (t80) cc_final: 0.8618 (t80) REVERT: A 389 ASP cc_start: 0.8739 (m-30) cc_final: 0.8477 (m-30) REVERT: A 420 ASP cc_start: 0.8715 (m-30) cc_final: 0.8187 (m-30) REVERT: A 489 TYR cc_start: 0.8719 (m-10) cc_final: 0.8421 (m-10) outliers start: 7 outliers final: 6 residues processed: 68 average time/residue: 0.1621 time to fit residues: 13.9335 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 : 0.422 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3431 Z= 0.308 Angle : 0.612 7.168 4667 Z= 0.314 Chirality : 0.046 0.139 497 Planarity : 0.004 0.041 611 Dihedral : 4.144 21.916 496 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.06 % Allowed : 15.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.41), residues: 424 helix: -2.88 (0.74), residues: 33 sheet: 0.85 (0.44), residues: 152 loop : -1.10 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.007 0.002 HIS A 519 PHE 0.009 0.001 PHE A 347 TYR 0.019 0.001 TYR H 53 ARG 0.002 0.000 ARG A 466 *********************** 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 75 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.363 Fit side-chains REVERT: L 16 GLN cc_start: 0.8417 (pm20) cc_final: 0.8182 (pm20) REVERT: L 85 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7579 (pm20) REVERT: H 56 ASN cc_start: 0.9239 (m110) cc_final: 0.8812 (m110) REVERT: H 73 ASP cc_start: 0.8013 (t0) cc_final: 0.7610 (t0) REVERT: A 389 ASP cc_start: 0.8816 (m-30) cc_final: 0.8566 (m-30) REVERT: A 420 ASP cc_start: 0.8727 (m-30) cc_final: 0.8158 (m-30) REVERT: A 489 TYR cc_start: 0.8792 (m-10) cc_final: 0.8563 (m-10) outliers start: 11 outliers final: 6 residues processed: 71 average time/residue: 0.1556 time to fit residues: 13.9340 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 : 0.379 ------------------------------------------------------------------------------- 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 22 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3431 Z= 0.192 Angle : 0.601 7.642 4667 Z= 0.306 Chirality : 0.044 0.131 497 Planarity : 0.003 0.041 611 Dihedral : 4.046 21.417 496 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.50 % Allowed : 15.00 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.41), residues: 424 helix: -2.84 (0.76), residues: 33 sheet: 0.90 (0.44), residues: 152 loop : -1.08 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.007 0.002 HIS A 519 PHE 0.009 0.001 PHE L 51 TYR 0.018 0.001 TYR H 53 ARG 0.001 0.000 ARG A 466 *********************** 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 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.402 Fit side-chains REVERT: L 16 GLN cc_start: 0.8439 (pm20) cc_final: 0.8200 (pm20) REVERT: L 85 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7601 (pm20) REVERT: H 56 ASN cc_start: 0.9251 (m110) cc_final: 0.8843 (m110) REVERT: H 73 ASP cc_start: 0.8001 (t0) cc_final: 0.7599 (t0) REVERT: A 389 ASP cc_start: 0.8779 (m-30) cc_final: 0.8537 (m-30) REVERT: A 420 ASP cc_start: 0.8701 (m-30) cc_final: 0.8139 (m-30) REVERT: A 489 TYR cc_start: 0.8803 (m-10) cc_final: 0.8573 (m-10) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.1501 time to fit residues: 13.2896 Evaluate side-chains 72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 18 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 119 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3431 Z= 0.195 Angle : 0.619 8.272 4667 Z= 0.310 Chirality : 0.045 0.129 497 Planarity : 0.003 0.040 611 Dihedral : 4.021 20.890 496 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.94 % Allowed : 17.22 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.41), residues: 424 helix: -2.84 (0.76), residues: 33 sheet: 0.93 (0.44), residues: 155 loop : -1.03 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.007 0.002 HIS A 519 PHE 0.009 0.001 PHE L 51 TYR 0.017 0.001 TYR H 53 ARG 0.001 0.000 ARG A 466 *********************** 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 74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.392 Fit side-chains REVERT: L 16 GLN cc_start: 0.8431 (pm20) cc_final: 0.8195 (pm20) REVERT: L 85 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7603 (pm20) REVERT: H 56 ASN cc_start: 0.9245 (m110) cc_final: 0.8830 (m110) REVERT: H 73 ASP cc_start: 0.8049 (t0) cc_final: 0.7653 (t0) REVERT: A 389 ASP cc_start: 0.8785 (m-30) cc_final: 0.8541 (m-30) REVERT: A 420 ASP cc_start: 0.8713 (m-30) cc_final: 0.8144 (m-30) REVERT: A 489 TYR cc_start: 0.8813 (m-10) cc_final: 0.8605 (m-10) outliers start: 7 outliers final: 6 residues processed: 70 average time/residue: 0.1621 time to fit residues: 13.8930 Evaluate side-chains 70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 22 CYS 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 20 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.0020 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.5948 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3431 Z= 0.164 Angle : 0.633 10.034 4667 Z= 0.315 Chirality : 0.044 0.130 497 Planarity : 0.003 0.040 611 Dihedral : 3.933 20.229 496 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.41), residues: 424 helix: -2.87 (0.75), residues: 33 sheet: 0.92 (0.43), residues: 155 loop : -0.98 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.007 0.002 HIS A 519 PHE 0.009 0.001 PHE L 51 TYR 0.016 0.001 TYR H 53 ARG 0.003 0.000 ARG A 403 ********************** 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 70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.400 Fit side-chains REVERT: L 85 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7606 (pm20) REVERT: H 56 ASN cc_start: 0.9244 (m110) cc_final: 0.8840 (m110) REVERT: H 73 ASP cc_start: 0.8058 (t0) cc_final: 0.7687 (t0) REVERT: A 389 ASP cc_start: 0.8750 (m-30) cc_final: 0.8497 (m-30) REVERT: A 420 ASP cc_start: 0.8704 (m-30) cc_final: 0.8134 (m-30) REVERT: A 489 TYR cc_start: 0.8786 (m-10) cc_final: 0.8578 (m-10) outliers start: 5 outliers final: 5 residues processed: 68 average time/residue: 0.1587 time to fit residues: 13.4976 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 : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 22 CYS 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 29 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.078403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.058137 restraints weight = 8192.948| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.78 r_work: 0.2608 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3431 Z= 0.203 Angle : 0.648 10.120 4667 Z= 0.322 Chirality : 0.045 0.163 497 Planarity : 0.004 0.039 611 Dihedral : 3.961 19.595 496 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.11 % Allowed : 18.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.41), residues: 424 helix: -2.84 (0.76), residues: 33 sheet: 0.93 (0.43), residues: 155 loop : -1.01 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.007 0.002 HIS A 519 PHE 0.009 0.001 PHE L 51 TYR 0.017 0.001 TYR H 53 ARG 0.001 0.000 ARG L 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1587.68 seconds wall clock time: 30 minutes 4.59 seconds (1804.59 seconds total)