Starting phenix.real_space_refine on Sun Mar 10 15:44:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs9_34226/03_2024/8gs9_34226.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs9_34226/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs9_34226/03_2024/8gs9_34226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs9_34226/03_2024/8gs9_34226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs9_34226/03_2024/8gs9_34226.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs9_34226/03_2024/8gs9_34226.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.15, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 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: 1.16 Conformation dependent library (CDL) restraints added in 557.1 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: 0.41 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: 0.82 Time building geometry restraints manager: 1.27 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: 100.85 - 107.47: 103 107.47 - 114.10: 1699 114.10 - 120.73: 1287 120.73 - 127.36: 1217 127.36 - 133.98: 29 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 2.520 nonbonded pdb=" N GLU H 6 " pdb=" OE1 GLU H 6 " model vdw 2.347 2.520 nonbonded pdb=" OH TYR A 473 " pdb=" O ARG H 31 " model vdw 2.378 2.440 nonbonded pdb=" NE ARG H 38 " pdb=" OE1 GLU H 46 " model vdw 2.428 2.520 nonbonded pdb=" N GLY H 15 " pdb=" O LEU H 85 " model vdw 2.437 2.520 ... (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 ========== 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.860 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.410 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:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.290 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.365 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: 1.0097 time to fit residues: 93.8064 Evaluate side-chains 52 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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: 6.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN K 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3194 Z= 0.183 Angle : 0.554 7.199 4335 Z= 0.301 Chirality : 0.045 0.168 461 Planarity : 0.004 0.026 564 Dihedral : 4.796 35.015 444 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.59 % Favored : 96.15 % Rotamer: Outliers : 5.97 % Allowed : 14.63 % Favored : 79.40 % 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: -0.24 (0.40), residues: 390 helix: -3.30 (0.88), residues: 20 sheet: 0.70 (0.48), residues: 111 loop : -0.25 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.001 0.000 HIS K 90 PHE 0.009 0.001 PHE A 456 TYR 0.010 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 75 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 55 time to evaluate : 0.338 Fit side-chains REVERT: A 456 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6810 (p90) REVERT: K 18 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.5742 (ttp-170) REVERT: K 83 PHE cc_start: 0.6049 (m-80) cc_final: 0.5700 (m-80) outliers start: 20 outliers final: 8 residues processed: 63 average time/residue: 0.9043 time to fit residues: 59.0600 Evaluate side-chains 56 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN K 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 3194 Z= 0.216 Angle : 0.571 8.669 4335 Z= 0.303 Chirality : 0.046 0.245 461 Planarity : 0.004 0.026 564 Dihedral : 4.809 35.408 444 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.85 % Favored : 95.90 % Rotamer: Outliers : 5.07 % Allowed : 15.82 % Favored : 79.10 % 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: -0.15 (0.41), residues: 390 helix: -3.37 (0.92), residues: 20 sheet: 0.54 (0.47), residues: 121 loop : -0.08 (0.37), residues: 249 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 0.012 0.001 PHE H 105 TYR 0.011 0.001 TYR H 52 ARG 0.006 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 73 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 56 time to evaluate : 0.359 Fit side-chains REVERT: A 456 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6831 (p90) REVERT: H 12 ILE cc_start: 0.3215 (OUTLIER) cc_final: 0.2358 (tp) REVERT: H 105 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: K 18 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.5665 (ttp-170) REVERT: K 83 PHE cc_start: 0.6282 (m-80) cc_final: 0.5928 (m-80) outliers start: 17 outliers final: 8 residues processed: 66 average time/residue: 0.8422 time to fit residues: 57.8007 Evaluate side-chains 61 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP 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 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 105 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3180 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 : 0.583 13.829 4335 Z= 0.303 Chirality : 0.045 0.265 461 Planarity : 0.003 0.025 564 Dihedral : 4.780 35.251 444 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: -0.11 (0.41), residues: 390 helix: -3.36 (0.94), residues: 20 sheet: 0.62 (0.48), residues: 124 loop : -0.08 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.000 0.000 HIS K 90 PHE 0.010 0.001 PHE H 105 TYR 0.009 0.001 TYR H 52 ARG 0.006 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 70 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 0.358 Fit side-chains REVERT: A 456 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6776 (p90) REVERT: H 12 ILE cc_start: 0.3122 (OUTLIER) cc_final: 0.2226 (tp) REVERT: H 20 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7224 (mm) REVERT: H 105 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.6773 (m-80) REVERT: K 18 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5688 (ttp-170) REVERT: K 83 PHE cc_start: 0.6378 (m-80) cc_final: 0.6035 (m-80) outliers start: 17 outliers final: 8 residues processed: 62 average time/residue: 0.8900 time to fit residues: 57.2576 Evaluate side-chains 61 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP 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 12 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 105 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 Chi-restraints excluded: chain K residue 96 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.0670 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3345 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= 0.198 Angle : 0.558 10.043 4335 Z= 0.291 Chirality : 0.045 0.225 461 Planarity : 0.003 0.023 564 Dihedral : 4.651 35.114 444 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.48 % Allowed : 19.40 % Favored : 76.12 % 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: -0.16 (0.41), residues: 390 helix: -3.42 (0.94), residues: 20 sheet: 0.78 (0.49), residues: 119 loop : -0.22 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 106 HIS 0.000 0.000 HIS K 90 PHE 0.011 0.001 PHE H 105 TYR 0.008 0.001 TYR H 52 ARG 0.006 0.000 ARG K 24 *********************** 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 66 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.367 Fit side-chains REVERT: A 456 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6748 (p90) REVERT: H 12 ILE cc_start: 0.3043 (OUTLIER) cc_final: 0.2158 (tp) REVERT: H 20 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7201 (mm) REVERT: K 18 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.5656 (ttp-170) outliers start: 15 outliers final: 5 residues processed: 59 average time/residue: 0.8999 time to fit residues: 55.1534 Evaluate side-chains 57 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 12 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 96 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 3194 Z= 0.271 Angle : 0.622 12.394 4335 Z= 0.322 Chirality : 0.046 0.209 461 Planarity : 0.004 0.027 564 Dihedral : 5.078 38.192 444 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.07 % Allowed : 20.30 % Favored : 74.63 % 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: -0.59 (0.41), residues: 390 helix: -3.31 (0.85), residues: 26 sheet: 0.48 (0.47), residues: 133 loop : -0.52 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.000 0.000 HIS K 90 PHE 0.008 0.001 PHE A 456 TYR 0.013 0.001 TYR H 52 ARG 0.002 0.000 ARG A 466 *********************** 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 65 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 0.329 Fit side-chains REVERT: A 456 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6886 (p90) REVERT: H 12 ILE cc_start: 0.3585 (OUTLIER) cc_final: 0.2609 (tp) REVERT: H 20 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7217 (mm) REVERT: K 18 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.5692 (ttp-170) outliers start: 17 outliers final: 7 residues processed: 57 average time/residue: 0.9140 time to fit residues: 54.0827 Evaluate side-chains 58 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP 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 12 ILE Chi-restraints excluded: chain H residue 20 LEU 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 Chi-restraints excluded: chain K residue 96 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.6978 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3194 Z= 0.186 Angle : 0.589 13.162 4335 Z= 0.307 Chirality : 0.045 0.233 461 Planarity : 0.003 0.024 564 Dihedral : 4.917 38.121 444 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.48 % Allowed : 21.49 % Favored : 74.03 % 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: -0.47 (0.41), residues: 390 helix: -3.31 (0.84), residues: 26 sheet: 0.81 (0.50), residues: 119 loop : -0.52 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.000 0.000 HIS A 505 PHE 0.008 0.001 PHE H 105 TYR 0.009 0.001 TYR H 52 ARG 0.001 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 66 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.361 Fit side-chains REVERT: A 456 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6834 (p90) REVERT: H 12 ILE cc_start: 0.3368 (OUTLIER) cc_final: 0.2418 (tp) REVERT: K 18 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.5621 (ttp-170) outliers start: 15 outliers final: 5 residues processed: 58 average time/residue: 0.9686 time to fit residues: 58.1958 Evaluate side-chains 56 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 12 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.0050 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3688 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= 0.310 Angle : 0.704 12.804 4335 Z= 0.362 Chirality : 0.047 0.236 461 Planarity : 0.004 0.028 564 Dihedral : 5.514 45.252 444 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.37 % Allowed : 20.90 % 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: -0.92 (0.41), residues: 390 helix: -3.32 (0.73), residues: 29 sheet: 0.34 (0.47), residues: 133 loop : -0.80 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 353 HIS 0.001 0.000 HIS K 90 PHE 0.011 0.001 PHE A 456 TYR 0.015 0.002 TYR H 52 ARG 0.003 0.001 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 64 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 46 time to evaluate : 0.391 Fit side-chains REVERT: A 456 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6814 (p90) REVERT: H 12 ILE cc_start: 0.3635 (OUTLIER) cc_final: 0.2686 (tp) REVERT: K 18 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.5808 (ttp-170) outliers start: 18 outliers final: 10 residues processed: 57 average time/residue: 0.9944 time to fit residues: 58.6966 Evaluate side-chains 56 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 389 ASP 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 12 ILE 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 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: 0.6980 chunk 34 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 108 GLN K 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3194 Z= 0.192 Angle : 0.614 12.272 4335 Z= 0.319 Chirality : 0.045 0.223 461 Planarity : 0.003 0.027 564 Dihedral : 5.081 44.672 444 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.18 % Allowed : 22.39 % Favored : 73.43 % 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: -3.25 (0.75), residues: 29 sheet: 0.37 (0.47), residues: 133 loop : -0.71 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.000 0.000 HIS A 505 PHE 0.010 0.001 PHE A 456 TYR 0.009 0.001 TYR H 52 ARG 0.002 0.000 ARG A 457 *********************** 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 61 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.389 Fit side-chains REVERT: A 456 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6874 (p90) REVERT: H 12 ILE cc_start: 0.3366 (OUTLIER) cc_final: 0.2404 (tp) REVERT: K 18 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.5622 (ttp-170) outliers start: 14 outliers final: 8 residues processed: 57 average time/residue: 0.9374 time to fit residues: 55.3953 Evaluate side-chains 56 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 12 ILE 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: 5.9990 chunk 24 optimal weight: 0.0570 chunk 32 optimal weight: 0.0670 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN K 38 GLN K 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3194 Z= 0.167 Angle : 0.587 11.681 4335 Z= 0.308 Chirality : 0.044 0.210 461 Planarity : 0.003 0.025 564 Dihedral : 4.630 40.532 444 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.88 % Allowed : 22.39 % 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: -0.56 (0.40), residues: 390 helix: -3.23 (0.74), residues: 29 sheet: 0.84 (0.50), residues: 119 loop : -0.62 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.000 0.000 HIS A 505 PHE 0.008 0.001 PHE H 105 TYR 0.006 0.001 TYR K 49 ARG 0.002 0.000 ARG A 357 ********************** 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 63 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.342 Fit side-chains REVERT: A 456 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6962 (p90) REVERT: H 12 ILE cc_start: 0.3003 (OUTLIER) cc_final: 0.2137 (tp) REVERT: K 18 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.5616 (ttp-170) outliers start: 13 outliers final: 9 residues processed: 58 average time/residue: 1.0635 time to fit residues: 63.8178 Evaluate side-chains 57 residues out of total 335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 12 ILE 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 38 GLN 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: 0.9980 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.0770 chunk 35 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 GLN K 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.146856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.134957 restraints weight = 6945.251| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.22 r_work: 0.4012 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3911 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= 0.192 Angle : 0.598 11.672 4335 Z= 0.312 Chirality : 0.044 0.212 461 Planarity : 0.003 0.024 564 Dihedral : 4.727 40.245 444 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.88 % Allowed : 22.69 % Favored : 73.43 % 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: -0.58 (0.40), residues: 390 helix: -3.23 (0.74), residues: 29 sheet: 0.91 (0.51), residues: 119 loop : -0.68 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.000 0.000 HIS K 90 PHE 0.008 0.001 PHE H 105 TYR 0.008 0.001 TYR H 52 ARG 0.003 0.000 ARG H 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1785.24 seconds wall clock time: 32 minutes 19.74 seconds (1939.74 seconds total)