Starting phenix.real_space_refine on Mon Jan 13 17:53:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yh6_33820/01_2025/7yh6_33820.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yh6_33820/01_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_33820/01_2025/7yh6_33820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yh6_33820/01_2025/7yh6_33820.map" model { file = "/net/cci-nas-00/data/ceres_data/7yh6_33820/01_2025/7yh6_33820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yh6_33820/01_2025/7yh6_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 5.28, per 1000 atoms: 1.58 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: 0.79 Conformation dependent library (CDL) restraints added in 577.1 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: 0.48 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: 0.88 Time building geometry restraints manager: 0.94 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: 7.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.870 Find NCS groups from input model: 0.080 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.640 ------------------------------------------------------------------------------- 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 : 0.523 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: 0.1683 time to fit residues: 14.1144 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 : 0.374 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.077884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.057242 restraints weight = 8081.868| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.86 r_work: 0.2586 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.378 Fit side-chains REVERT: L 85 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7354 (pm20) REVERT: H 43 LYS cc_start: 0.8323 (mmmt) cc_final: 0.8098 (mmmt) REVERT: H 56 ASN cc_start: 0.9293 (m110) cc_final: 0.8925 (m110) REVERT: H 73 ASP cc_start: 0.8069 (t0) cc_final: 0.7630 (t0) REVERT: A 420 ASP cc_start: 0.9062 (m-30) cc_final: 0.8641 (m-30) REVERT: A 489 TYR cc_start: 0.8865 (m-10) cc_final: 0.8663 (m-10) REVERT: A 525 CYS cc_start: 0.6523 (p) cc_final: 0.6302 (p) outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 0.1555 time to fit residues: 12.9899 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 : 0.360 ------------------------------------------------------------------------------- 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 34 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.077198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.056695 restraints weight = 8116.598| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.81 r_work: 0.2567 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3431 Z= 0.244 Angle : 0.593 9.360 4667 Z= 0.304 Chirality : 0.046 0.133 497 Planarity : 0.004 0.041 611 Dihedral : 4.396 29.069 496 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.66 % Favored : 94.10 % 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 (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: -0.93 (0.41), residues: 424 helix: -3.13 (0.68), residues: 33 sheet: 0.74 (0.44), residues: 152 loop : -1.19 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.005 0.002 HIS A 519 PHE 0.010 0.001 PHE A 347 TYR 0.019 0.001 TYR H 53 ARG 0.002 0.000 ARG A 466 *********************** 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 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.371 Fit side-chains REVERT: L 85 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7452 (pm20) REVERT: H 43 LYS cc_start: 0.8264 (mmmt) cc_final: 0.8002 (mmmt) REVERT: H 56 ASN cc_start: 0.9309 (m110) cc_final: 0.8930 (m110) REVERT: H 73 ASP cc_start: 0.7928 (t0) cc_final: 0.7516 (t0) REVERT: H 117 GLN cc_start: 0.9122 (tp40) cc_final: 0.8902 (mm110) REVERT: A 420 ASP cc_start: 0.9064 (m-30) cc_final: 0.8599 (m-30) REVERT: A 489 TYR cc_start: 0.8891 (m-10) cc_final: 0.8657 (m-10) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 0.1524 time to fit residues: 12.1133 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 : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.075612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.055151 restraints weight = 8332.144| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 3.75 r_work: 0.2546 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3431 Z= 0.342 Angle : 0.631 9.152 4667 Z= 0.323 Chirality : 0.047 0.137 497 Planarity : 0.004 0.041 611 Dihedral : 4.484 26.366 496 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.37 % Favored : 93.40 % Rotamer: Outliers : 2.22 % Allowed : 13.61 % Favored : 84.17 % 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: -1.02 (0.41), residues: 424 helix: -2.97 (0.72), residues: 33 sheet: 0.63 (0.44), residues: 152 loop : -1.25 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.006 0.002 HIS A 519 PHE 0.010 0.001 PHE A 347 TYR 0.018 0.001 TYR H 53 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.391 Fit side-chains REVERT: L 85 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7572 (pm20) REVERT: H 43 LYS cc_start: 0.8313 (mmmt) cc_final: 0.8069 (mmmt) REVERT: H 56 ASN cc_start: 0.9301 (m110) cc_final: 0.8887 (m110) REVERT: H 73 ASP cc_start: 0.8039 (t0) cc_final: 0.7635 (t0) REVERT: A 420 ASP cc_start: 0.9072 (m-30) cc_final: 0.8580 (m-30) REVERT: A 489 TYR cc_start: 0.8971 (m-10) cc_final: 0.8759 (m-10) outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.1490 time to fit residues: 12.0408 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 : 0.364 ------------------------------------------------------------------------------- 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 21 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.077619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.057076 restraints weight = 8176.455| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.84 r_work: 0.2583 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3431 Z= 0.184 Angle : 0.565 8.175 4667 Z= 0.289 Chirality : 0.044 0.131 497 Planarity : 0.004 0.041 611 Dihedral : 4.238 25.067 496 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.67 % Allowed : 16.94 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.94 (0.41), residues: 424 helix: -2.93 (0.73), residues: 33 sheet: 0.65 (0.44), residues: 152 loop : -1.15 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.006 0.002 HIS A 519 PHE 0.010 0.001 PHE L 51 TYR 0.018 0.001 TYR H 53 ARG 0.003 0.000 ARG L 44 *********************** 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 70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.328 Fit side-chains REVERT: L 85 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7615 (pm20) REVERT: H 43 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7926 (mmmt) REVERT: H 56 ASN cc_start: 0.9313 (m110) cc_final: 0.8915 (m110) REVERT: H 73 ASP cc_start: 0.7851 (t0) cc_final: 0.7422 (t0) REVERT: A 420 ASP cc_start: 0.9056 (m-30) cc_final: 0.8547 (m-30) outliers start: 6 outliers final: 3 residues processed: 68 average time/residue: 0.1568 time to fit residues: 13.1205 Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3127 r_free = 0.3127 target = 0.076616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.056271 restraints weight = 8424.834| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.75 r_work: 0.2569 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3431 Z= 0.254 Angle : 0.595 8.620 4667 Z= 0.306 Chirality : 0.045 0.145 497 Planarity : 0.004 0.040 611 Dihedral : 4.276 23.934 496 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % 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: -0.98 (0.41), residues: 424 helix: -2.91 (0.73), residues: 33 sheet: 0.58 (0.44), residues: 152 loop : -1.16 (0.40), 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 0.010 0.001 PHE L 51 TYR 0.018 0.001 TYR H 53 ARG 0.002 0.000 ARG A 466 *********************** 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: 7 poor density : 64 time to evaluate : 0.400 Fit side-chains REVERT: L 85 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7696 (pm20) REVERT: H 43 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7984 (mmmt) REVERT: H 56 ASN cc_start: 0.9313 (m110) cc_final: 0.8894 (m110) REVERT: H 73 ASP cc_start: 0.8001 (t0) cc_final: 0.7594 (t0) REVERT: A 420 ASP cc_start: 0.9058 (m-30) cc_final: 0.8561 (m-30) outliers start: 7 outliers final: 4 residues processed: 67 average time/residue: 0.1655 time to fit residues: 13.5754 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 : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.9942 ------------------------------------------------------------------------------- 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 = 0.3137 r_free = 0.3137 target = 0.077203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.057106 restraints weight = 8238.841| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.70 r_work: 0.2590 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3431 Z= 0.201 Angle : 0.584 8.352 4667 Z= 0.298 Chirality : 0.045 0.146 497 Planarity : 0.004 0.040 611 Dihedral : 4.181 23.375 496 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.67 % Allowed : 16.94 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.93 (0.41), residues: 424 helix: -2.88 (0.74), residues: 33 sheet: 0.63 (0.44), residues: 152 loop : -1.15 (0.40), 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 0.010 0.001 PHE L 51 TYR 0.018 0.001 TYR H 53 ARG 0.002 0.000 ARG L 44 *********************** 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 73 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.376 Fit side-chains REVERT: L 85 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7721 (pm20) REVERT: H 56 ASN cc_start: 0.9311 (m110) cc_final: 0.8898 (m110) REVERT: H 73 ASP cc_start: 0.8010 (t0) cc_final: 0.7630 (t0) REVERT: A 420 ASP cc_start: 0.9047 (m-30) cc_final: 0.8543 (m-30) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.1574 time to fit residues: 13.3920 Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 392 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.7571 > 50: distance: 17 - 149: 15.142 distance: 20 - 146: 12.631 distance: 32 - 132: 10.327 distance: 35 - 129: 22.412 distance: 77 - 140: 10.190 distance: 80 - 137: 8.736 distance: 90 - 120: 15.026 distance: 93 - 117: 8.214 distance: 112 - 117: 11.269 distance: 117 - 118: 5.395 distance: 118 - 119: 19.717 distance: 118 - 121: 5.050 distance: 119 - 120: 4.604 distance: 119 - 129: 6.349 distance: 121 - 122: 10.406 distance: 122 - 123: 21.064 distance: 122 - 124: 9.880 distance: 123 - 125: 19.540 distance: 124 - 126: 12.690 distance: 126 - 127: 8.961 distance: 127 - 128: 12.523 distance: 129 - 130: 17.352 distance: 130 - 131: 13.971 distance: 130 - 133: 14.916 distance: 131 - 132: 6.520 distance: 131 - 137: 17.046 distance: 133 - 134: 17.740 distance: 134 - 135: 20.587 distance: 134 - 136: 15.210 distance: 137 - 138: 6.276 distance: 138 - 139: 7.272 distance: 138 - 141: 12.374 distance: 139 - 140: 4.404 distance: 139 - 146: 15.889 distance: 141 - 142: 17.751 distance: 142 - 143: 9.335 distance: 143 - 144: 6.577 distance: 146 - 147: 5.265 distance: 147 - 148: 13.431 distance: 147 - 150: 18.150 distance: 148 - 149: 10.011 distance: 148 - 154: 5.710 distance: 150 - 151: 4.932 distance: 151 - 152: 18.159 distance: 152 - 153: 10.030 distance: 154 - 155: 9.520 distance: 155 - 156: 11.369 distance: 155 - 158: 9.920 distance: 156 - 157: 11.747 distance: 156 - 162: 16.447 distance: 158 - 159: 7.245 distance: 159 - 160: 5.297 distance: 159 - 161: 4.696 distance: 162 - 163: 18.116 distance: 163 - 164: 20.461 distance: 163 - 166: 29.170 distance: 164 - 165: 26.431 distance: 164 - 168: 29.418 distance: 166 - 167: 21.941 distance: 168 - 169: 17.377 distance: 169 - 170: 23.598 distance: 169 - 172: 6.682 distance: 170 - 171: 34.612 distance: 170 - 176: 38.977 distance: 172 - 173: 10.974 distance: 173 - 174: 16.599 distance: 173 - 175: 31.151 distance: 177 - 178: 38.415 distance: 178 - 179: 9.784 distance: 178 - 180: 17.664 distance: 179 - 196: 30.077 distance: 180 - 181: 16.800 distance: 180 - 186: 14.464 distance: 181 - 182: 5.591 distance: 181 - 184: 9.813 distance: 182 - 183: 21.159 distance: 182 - 187: 10.832 distance: 184 - 185: 16.309 distance: 185 - 186: 20.830 distance: 187 - 188: 15.751 distance: 188 - 189: 6.388 distance: 188 - 191: 15.061 distance: 189 - 190: 29.235 distance: 189 - 196: 8.612 distance: 191 - 192: 20.898 distance: 192 - 193: 14.515 distance: 193 - 194: 16.117 distance: 193 - 195: 9.543