Starting phenix.real_space_refine on Fri Dec 27 06:09:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gs9_34226/12_2024/8gs9_34226.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gs9_34226/12_2024/8gs9_34226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gs9_34226/12_2024/8gs9_34226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gs9_34226/12_2024/8gs9_34226.map" model { file = "/net/cci-nas-00/data/ceres_data/8gs9_34226/12_2024/8gs9_34226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gs9_34226/12_2024/8gs9_34226.cif" } resolution = 2.66 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= -0.003 sd= 0.041 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 12 5.16 5 C 1984 2.51 5 N 531 2.21 5 O 589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3116 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1462 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 171} Chain: "H" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 881 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "K" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 773 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 96} Time building chain proxies: 3.45, per 1000 atoms: 1.11 Number of scatterers: 3116 At special positions: 0 Unit cell: (67.545, 58.995, 94.905, 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 12 16.00 O 589 8.00 N 531 7.00 C 1984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 357.2 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 724 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 12.1% alpha, 38.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.143A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 371' Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.515A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.017A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.954A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR H 33 " --> pdb=" O SER H 98 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE H 105 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR H 33 " --> pdb=" O SER H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.535A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 11 through 12 130 hydrogen bonds defined for protein. 300 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: 0.81 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1009 1.34 - 1.46: 845 1.46 - 1.58: 1326 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 3194 Sorted by residual: bond pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 8.98e+00 bond pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.39e+00 bond pdb=" N CYS A 361 " pdb=" CA CYS A 361 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.26e-02 6.30e+03 6.87e+00 bond pdb=" N SER A 359 " pdb=" CA SER A 359 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.81e+00 bond pdb=" N ALA A 363 " pdb=" CA ALA A 363 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.24e-02 6.50e+03 4.10e+00 ... (remaining 3189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 4007 0.92 - 1.84: 260 1.84 - 2.76: 45 2.76 - 3.68: 18 3.68 - 4.60: 5 Bond angle restraints: 4335 Sorted by residual: angle pdb=" CA VAL A 362 " pdb=" C VAL A 362 " pdb=" O VAL A 362 " ideal model delta sigma weight residual 121.36 117.47 3.89 1.10e+00 8.26e-01 1.25e+01 angle pdb=" N ALA K 51 " pdb=" CA ALA K 51 " pdb=" CB ALA K 51 " ideal model delta sigma weight residual 114.17 110.62 3.55 1.14e+00 7.69e-01 9.68e+00 angle pdb=" CA SER A 359 " pdb=" C SER A 359 " pdb=" O SER A 359 " ideal model delta sigma weight residual 120.51 116.68 3.83 1.43e+00 4.89e-01 7.17e+00 angle pdb=" C ASN A 450 " pdb=" N TYR A 451 " pdb=" CA TYR A 451 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.80e+00 angle pdb=" CA ALA A 363 " pdb=" C ALA A 363 " pdb=" O ALA A 363 " ideal model delta sigma weight residual 120.32 117.78 2.54 1.11e+00 8.12e-01 5.25e+00 ... (remaining 4330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.49: 1681 13.49 - 26.98: 138 26.98 - 40.48: 38 40.48 - 53.97: 9 53.97 - 67.46: 6 Dihedral angle restraints: 1872 sinusoidal: 729 harmonic: 1143 Sorted by residual: dihedral pdb=" CA PHE A 490 " pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta harmonic sigma weight residual -180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA GLN H 13 " pdb=" C GLN H 13 " pdb=" N PRO H 14 " pdb=" CA PRO H 14 " ideal model delta harmonic sigma weight residual 180.00 -163.10 -16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA LYS A 478 " pdb=" C LYS A 478 " pdb=" N PRO A 479 " pdb=" CA PRO A 479 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 1869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 300 0.035 - 0.070: 109 0.070 - 0.105: 30 0.105 - 0.140: 20 0.140 - 0.175: 2 Chirality restraints: 461 Sorted by residual: chirality pdb=" CA VAL A 362 " pdb=" N VAL A 362 " pdb=" C VAL A 362 " pdb=" CB VAL A 362 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE K 21 " pdb=" N ILE K 21 " pdb=" C ILE K 21 " pdb=" CB ILE K 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 458 not shown) Planarity restraints: 564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 358 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C ILE A 358 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE A 358 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 359 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 478 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO A 479 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 32 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C ASN H 32 " 0.020 2.00e-02 2.50e+03 pdb=" O ASN H 32 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR H 33 " -0.007 2.00e-02 2.50e+03 ... (remaining 561 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 940 2.82 - 3.34: 2496 3.34 - 3.86: 4712 3.86 - 4.38: 5702 4.38 - 4.90: 10174 Nonbonded interactions: 24024 Sorted by model distance: nonbonded pdb=" NE2 GLN K 89 " pdb=" O GLU K 91 " model vdw 2.297 3.120 nonbonded pdb=" N GLU H 6 " pdb=" OE1 GLU H 6 " model vdw 2.347 3.120 nonbonded pdb=" OH TYR A 473 " pdb=" O ARG H 31 " model vdw 2.378 3.040 nonbonded pdb=" NE ARG H 38 " pdb=" OE1 GLU H 46 " model vdw 2.428 3.120 nonbonded pdb=" N GLY H 15 " pdb=" O LEU H 85 " model vdw 2.437 3.120 ... (remaining 24019 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3194 Z= 0.216 Angle : 0.547 4.601 4335 Z= 0.320 Chirality : 0.045 0.175 461 Planarity : 0.003 0.034 564 Dihedral : 11.977 67.459 1136 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.64 % Favored : 93.85 % Rotamer: Outliers : 0.60 % Allowed : 5.37 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.51 (0.40), residues: 390 helix: -3.37 (0.74), residues: 27 sheet: 0.37 (0.44), residues: 124 loop : -0.30 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS A 505 PHE 0.008 0.001 PHE A 456 TYR 0.007 0.001 TYR H 52 ARG 0.002 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.361 Fit side-chains REVERT: A 456 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6797 (p90) REVERT: A 516 GLU cc_start: 0.6176 (mt-10) cc_final: 0.5760 (mt-10) REVERT: K 83 PHE cc_start: 0.5818 (m-80) cc_final: 0.5538 (m-80) outliers start: 2 outliers final: 0 residues processed: 90 average time/residue: 1.0092 time to fit residues: 93.7013 Evaluate side-chains 52 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.0570 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN H 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3194 Z= 0.171 Angle : 0.541 7.273 4335 Z= 0.296 Chirality : 0.045 0.157 461 Planarity : 0.004 0.025 564 Dihedral : 4.637 32.022 444 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.33 % Favored : 96.41 % Rotamer: Outliers : 4.78 % Allowed : 15.22 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.39 (0.41), residues: 390 helix: -3.33 (0.73), residues: 26 sheet: 0.59 (0.48), residues: 113 loop : -0.28 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS K 90 PHE 0.008 0.001 PHE A 456 TYR 0.009 0.001 TYR H 52 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.340 Fit side-chains REVERT: A 456 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6561 (p90) REVERT: K 18 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.5716 (ttp-170) REVERT: K 83 PHE cc_start: 0.6097 (m-80) cc_final: 0.5783 (m-80) outliers start: 16 outliers final: 7 residues processed: 64 average time/residue: 0.9406 time to fit residues: 62.3676 Evaluate side-chains 57 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 3194 Z= 0.370 Angle : 0.717 8.584 4335 Z= 0.378 Chirality : 0.049 0.268 461 Planarity : 0.005 0.033 564 Dihedral : 5.532 44.108 444 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.87 % Favored : 94.87 % Rotamer: Outliers : 5.07 % Allowed : 17.61 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.75 (0.41), residues: 390 helix: -3.42 (0.75), residues: 26 sheet: 0.12 (0.45), residues: 135 loop : -0.45 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 353 HIS 0.001 0.000 HIS K 90 PHE 0.015 0.002 PHE H 105 TYR 0.019 0.002 TYR H 52 ARG 0.007 0.001 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.372 Fit side-chains REVERT: A 456 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6756 (p90) REVERT: H 20 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7239 (mm) REVERT: K 18 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.5687 (ttp-170) outliers start: 17 outliers final: 8 residues processed: 62 average time/residue: 0.9944 time to fit residues: 63.9289 Evaluate side-chains 55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 3194 Z= 0.212 Angle : 0.594 13.873 4335 Z= 0.313 Chirality : 0.046 0.258 461 Planarity : 0.004 0.028 564 Dihedral : 5.014 42.194 444 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.78 % Allowed : 18.51 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.47 (0.41), residues: 390 helix: -3.34 (0.81), residues: 26 sheet: 0.54 (0.49), residues: 124 loop : -0.38 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.000 0.000 HIS K 90 PHE 0.010 0.001 PHE A 456 TYR 0.010 0.001 TYR H 52 ARG 0.007 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.351 Fit side-chains REVERT: A 456 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6811 (p90) REVERT: H 20 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7238 (mm) REVERT: K 18 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5661 (ttp-170) outliers start: 16 outliers final: 7 residues processed: 61 average time/residue: 0.9036 time to fit residues: 57.2701 Evaluate side-chains 55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 105 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 3194 Z= 0.281 Angle : 0.643 10.217 4335 Z= 0.334 Chirality : 0.046 0.237 461 Planarity : 0.004 0.028 564 Dihedral : 5.258 46.914 444 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.07 % Allowed : 21.19 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.66 (0.41), residues: 390 helix: -3.40 (0.80), residues: 26 sheet: 0.34 (0.47), residues: 133 loop : -0.50 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 353 HIS 0.001 0.000 HIS K 90 PHE 0.012 0.001 PHE A 456 TYR 0.014 0.001 TYR H 52 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.375 Fit side-chains REVERT: A 456 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.6695 (p90) REVERT: H 20 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7283 (mm) REVERT: K 18 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.5710 (ttp-170) REVERT: K 38 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7442 (tt0) outliers start: 17 outliers final: 9 residues processed: 62 average time/residue: 0.9742 time to fit residues: 62.5815 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 105 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 3194 Z= 0.214 Angle : 0.613 12.175 4335 Z= 0.319 Chirality : 0.044 0.189 461 Planarity : 0.003 0.026 564 Dihedral : 5.021 45.957 444 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.07 % Allowed : 22.09 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.61 (0.42), residues: 390 helix: -3.36 (0.81), residues: 26 sheet: 0.40 (0.47), residues: 133 loop : -0.48 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 PHE 0.011 0.001 PHE A 456 TYR 0.008 0.001 TYR H 52 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.383 Fit side-chains REVERT: A 456 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6812 (p90) REVERT: H 20 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7258 (mm) REVERT: K 18 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.5564 (ttp-170) REVERT: K 82 ASP cc_start: 0.5918 (m-30) cc_final: 0.5706 (m-30) outliers start: 17 outliers final: 8 residues processed: 57 average time/residue: 1.0065 time to fit residues: 59.4126 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 105 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 37 optimal weight: 0.2980 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3194 Z= 0.233 Angle : 0.651 13.464 4335 Z= 0.337 Chirality : 0.046 0.236 461 Planarity : 0.004 0.026 564 Dihedral : 5.225 48.472 444 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.78 % Allowed : 22.99 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.79 (0.41), residues: 390 helix: -3.34 (0.72), residues: 29 sheet: 0.39 (0.48), residues: 133 loop : -0.67 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 PHE 0.012 0.001 PHE A 456 TYR 0.011 0.001 TYR H 52 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.370 Fit side-chains REVERT: A 389 ASP cc_start: 0.6739 (m-30) cc_final: 0.6520 (m-30) REVERT: H 20 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7292 (mm) REVERT: K 18 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.5662 (ttp-170) REVERT: K 82 ASP cc_start: 0.5915 (m-30) cc_final: 0.5709 (m-30) outliers start: 16 outliers final: 10 residues processed: 57 average time/residue: 1.0285 time to fit residues: 60.7003 Evaluate side-chains 53 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3194 Z= 0.292 Angle : 0.707 12.803 4335 Z= 0.369 Chirality : 0.047 0.237 461 Planarity : 0.004 0.029 564 Dihedral : 5.689 57.273 444 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.07 % Allowed : 23.58 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.01 (0.41), residues: 390 helix: -3.48 (0.68), residues: 29 sheet: 0.33 (0.48), residues: 133 loop : -0.89 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.001 0.001 HIS K 90 PHE 0.014 0.001 PHE A 456 TYR 0.014 0.002 TYR H 52 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.371 Fit side-chains REVERT: H 20 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7313 (mm) REVERT: K 18 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.5772 (ttp-170) REVERT: K 82 ASP cc_start: 0.5991 (m-30) cc_final: 0.5777 (m-30) outliers start: 17 outliers final: 11 residues processed: 56 average time/residue: 1.0672 time to fit residues: 61.8357 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.0970 chunk 34 optimal weight: 0.0570 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3194 Z= 0.183 Angle : 0.636 12.157 4335 Z= 0.337 Chirality : 0.045 0.213 461 Planarity : 0.004 0.034 564 Dihedral : 5.235 57.758 444 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.88 % Allowed : 24.48 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.68 (0.40), residues: 390 helix: -3.22 (0.76), residues: 29 sheet: 1.10 (0.54), residues: 109 loop : -0.85 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS K 90 PHE 0.012 0.001 PHE A 456 TYR 0.007 0.001 TYR H 33 ARG 0.008 0.000 ARG K 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7274 (mm) REVERT: K 18 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.5578 (ttp-170) outliers start: 13 outliers final: 10 residues processed: 59 average time/residue: 1.0921 time to fit residues: 66.5428 Evaluate side-chains 57 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3194 Z= 0.258 Angle : 0.687 12.115 4335 Z= 0.362 Chirality : 0.046 0.224 461 Planarity : 0.004 0.029 564 Dihedral : 5.436 55.711 444 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.18 % Allowed : 24.78 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 390 helix: -3.20 (0.79), residues: 29 sheet: 0.40 (0.49), residues: 133 loop : -0.88 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.001 0.000 HIS K 90 PHE 0.015 0.001 PHE A 456 TYR 0.012 0.001 TYR H 52 ARG 0.007 0.001 ARG K 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: H 20 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7300 (mm) REVERT: K 18 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.5693 (ttp-170) outliers start: 14 outliers final: 9 residues processed: 54 average time/residue: 1.0863 time to fit residues: 60.6450 Evaluate side-chains 54 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.146138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.134090 restraints weight = 6745.899| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.20 r_work: 0.4000 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3194 Z= 0.212 Angle : 0.662 12.078 4335 Z= 0.348 Chirality : 0.045 0.222 461 Planarity : 0.004 0.027 564 Dihedral : 5.191 51.877 444 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.48 % Allowed : 25.37 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.82 (0.41), residues: 390 helix: -3.12 (0.81), residues: 29 sheet: 0.44 (0.49), residues: 133 loop : -0.78 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.001 HIS K 90 PHE 0.013 0.001 PHE A 456 TYR 0.008 0.001 TYR H 52 ARG 0.007 0.000 ARG K 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1807.75 seconds wall clock time: 32 minutes 53.29 seconds (1973.29 seconds total)