Starting phenix.real_space_refine on Mon Sep 23 14:42:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wog_32651/09_2024/7wog_32651.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wog_32651/09_2024/7wog_32651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wog_32651/09_2024/7wog_32651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wog_32651/09_2024/7wog_32651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wog_32651/09_2024/7wog_32651.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wog_32651/09_2024/7wog_32651.cif" } resolution = 4.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 16 5.16 5 C 2122 2.51 5 N 569 2.21 5 O 655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3362 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1580 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 184} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 937 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "B" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 845 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Time building chain proxies: 2.92, per 1000 atoms: 0.87 Number of scatterers: 3362 At special positions: 0 Unit cell: (69.16, 91.504, 87.248, 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 16 16.00 O 655 8.00 N 569 7.00 C 2122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 91 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 475.7 milliseconds 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 794 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 7 sheets defined 6.5% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.591A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.831A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.841A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.962A pdb=" N THR A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.909A pdb=" N GLU B 86 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AA2, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.174A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 21 Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.756A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET A 34 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.520A pdb=" N TYR B 90 " --> pdb=" O TYR B 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 82 hydrogen bonds defined for protein. 189 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: 0.94 Time building geometry restraints manager: 1.26 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: 1085 1.34 - 1.46: 897 1.46 - 1.58: 1446 1.58 - 1.70: 0 1.70 - 1.81: 20 Bond restraints: 3448 Sorted by residual: bond pdb=" N GLY C 504 " pdb=" CA GLY C 504 " ideal model delta sigma weight residual 1.454 1.444 0.010 1.79e-02 3.12e+03 3.09e-01 bond pdb=" C LYS C 462 " pdb=" N PRO C 463 " ideal model delta sigma weight residual 1.334 1.346 -0.012 2.34e-02 1.83e+03 2.72e-01 bond pdb=" C LYS A 76 " pdb=" N ASN A 77 " ideal model delta sigma weight residual 1.331 1.337 -0.006 1.29e-02 6.01e+03 2.23e-01 bond pdb=" N ASN A 77 " pdb=" CA ASN A 77 " ideal model delta sigma weight residual 1.457 1.462 -0.005 1.31e-02 5.83e+03 1.73e-01 bond pdb=" CZ ARG B 112 " pdb=" NH2 ARG B 112 " ideal model delta sigma weight residual 1.330 1.325 0.005 1.30e-02 5.92e+03 1.69e-01 ... (remaining 3443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.65: 4288 0.65 - 1.29: 302 1.29 - 1.94: 64 1.94 - 2.59: 21 2.59 - 3.24: 14 Bond angle restraints: 4689 Sorted by residual: angle pdb=" C LYS A 76 " pdb=" N ASN A 77 " pdb=" CA ASN A 77 " ideal model delta sigma weight residual 121.56 124.80 -3.24 1.56e+00 4.11e-01 4.30e+00 angle pdb=" N ASN A 77 " pdb=" CA ASN A 77 " pdb=" C ASN A 77 " ideal model delta sigma weight residual 110.42 112.79 -2.37 1.46e+00 4.69e-01 2.64e+00 angle pdb=" NE ARG C 357 " pdb=" CZ ARG C 357 " pdb=" NH1 ARG C 357 " ideal model delta sigma weight residual 121.50 120.03 1.47 1.00e+00 1.00e+00 2.16e+00 angle pdb=" NE ARG B 40 " pdb=" CZ ARG B 40 " pdb=" NH1 ARG B 40 " ideal model delta sigma weight residual 121.50 120.05 1.45 1.00e+00 1.00e+00 2.09e+00 angle pdb=" NE ARG C 457 " pdb=" CZ ARG C 457 " pdb=" NH1 ARG C 457 " ideal model delta sigma weight residual 121.50 120.06 1.44 1.00e+00 1.00e+00 2.08e+00 ... (remaining 4684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.09: 1876 11.09 - 22.19: 114 22.19 - 33.28: 30 33.28 - 44.37: 10 44.37 - 55.46: 3 Dihedral angle restraints: 2033 sinusoidal: 779 harmonic: 1254 Sorted by residual: dihedral pdb=" CA LYS A 76 " pdb=" C LYS A 76 " pdb=" N ASN A 77 " pdb=" CA ASN A 77 " ideal model delta harmonic sigma weight residual 180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" N ARG C 457 " pdb=" CA ARG C 457 " pdb=" CB ARG C 457 " pdb=" CG ARG C 457 " ideal model delta sinusoidal sigma weight residual -180.00 -124.54 -55.46 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" CA CYS A 22 " pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " ideal model delta sinusoidal sigma weight residual -73.00 -124.56 51.56 1 2.00e+01 2.50e-03 9.08e+00 ... (remaining 2030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 293 0.026 - 0.052: 130 0.052 - 0.079: 35 0.079 - 0.105: 28 0.105 - 0.131: 16 Chirality restraints: 502 Sorted by residual: chirality pdb=" CA ILE B 67 " pdb=" N ILE B 67 " pdb=" C ILE B 67 " pdb=" CB ILE B 67 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE B 49 " pdb=" N ILE B 49 " pdb=" C ILE B 49 " pdb=" CB ILE B 49 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CB VAL C 433 " pdb=" CA VAL C 433 " pdb=" CG1 VAL C 433 " pdb=" CG2 VAL C 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 499 not shown) Planarity restraints: 609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO C 373 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 6 " -0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO B 7 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " 0.016 5.00e-02 4.00e+02 2.35e-02 8.82e-01 pdb=" N PRO C 337 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " 0.013 5.00e-02 4.00e+02 ... (remaining 606 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1012 2.81 - 3.34: 2783 3.34 - 3.86: 5344 3.86 - 4.38: 5893 4.38 - 4.90: 10189 Nonbonded interactions: 25221 Sorted by model distance: nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.293 3.040 nonbonded pdb=" O TRP C 353 " pdb=" OH TYR A 106 " model vdw 2.316 3.040 nonbonded pdb=" O SER A 31 " pdb=" OG SER A 102 " model vdw 2.343 3.040 nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.352 3.040 nonbonded pdb=" NH1 ARG A 67 " pdb=" O SER A 85 " model vdw 2.360 3.120 ... (remaining 25216 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 group one per residue 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: 0.760 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: 0.020 Set scattering table: 0.040 Process input model: 14.220 Find NCS groups from input model: 0.040 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5154 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 : 0.001 0.013 3448 Z= 0.091 Angle : 0.415 3.236 4689 Z= 0.239 Chirality : 0.041 0.131 502 Planarity : 0.003 0.032 609 Dihedral : 8.085 55.464 1221 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.78 % Allowed : 6.76 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.34), residues: 427 helix: None (None), residues: 0 sheet: -1.23 (0.39), residues: 126 loop : -3.58 (0.30), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 103 HIS 0.001 0.000 HIS B 99 PHE 0.004 0.000 PHE C 490 TYR 0.008 0.001 TYR A 59 ARG 0.001 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 338 PHE cc_start: 0.6498 (m-10) cc_final: 0.5856 (m-10) REVERT: C 358 ILE cc_start: 0.6075 (mm) cc_final: 0.5858 (mm) REVERT: C 380 TYR cc_start: 0.7645 (m-80) cc_final: 0.7217 (m-80) REVERT: C 408 ARG cc_start: 0.6717 (ptm-80) cc_final: 0.5396 (mmm-85) REVERT: C 452 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7789 (pt) REVERT: A 4 LEU cc_start: 0.0399 (OUTLIER) cc_final: 0.0053 (tm) REVERT: A 11 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6667 (pp) REVERT: A 34 MET cc_start: 0.6625 (mmm) cc_final: 0.6264 (mmm) REVERT: A 83 MET cc_start: 0.5214 (mtp) cc_final: 0.3636 (mtp) REVERT: B 102 PHE cc_start: 0.6892 (m-80) cc_final: 0.6553 (m-10) REVERT: B 106 THR cc_start: 0.7464 (m) cc_final: 0.7132 (p) outliers start: 14 outliers final: 3 residues processed: 98 average time/residue: 0.2357 time to fit residues: 26.3691 Evaluate side-chains 86 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.0270 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN C 354 ASN C 409 GLN C 437 ASN C 448 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 98 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5342 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3448 Z= 0.241 Angle : 0.602 5.659 4689 Z= 0.327 Chirality : 0.045 0.171 502 Planarity : 0.005 0.041 609 Dihedral : 4.300 20.666 481 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % Rotamer: Outliers : 0.27 % Allowed : 4.05 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.37), residues: 427 helix: -5.23 (0.46), residues: 7 sheet: -0.65 (0.43), residues: 129 loop : -3.03 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 103 HIS 0.002 0.001 HIS C 505 PHE 0.014 0.002 PHE C 377 TYR 0.027 0.002 TYR A 106 ARG 0.005 0.001 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 457 ARG cc_start: 0.6795 (tpp80) cc_final: 0.6343 (tpp80) REVERT: C 471 GLU cc_start: 0.7586 (pm20) cc_final: 0.7020 (pm20) REVERT: A 34 MET cc_start: 0.6639 (mmm) cc_final: 0.5395 (mmp) REVERT: A 51 ILE cc_start: 0.7660 (tt) cc_final: 0.7417 (tt) REVERT: A 67 ARG cc_start: 0.7313 (mtm110) cc_final: 0.6893 (mtp180) REVERT: A 74 ASN cc_start: 0.7243 (m-40) cc_final: 0.7041 (m-40) REVERT: A 77 ASN cc_start: 0.6590 (p0) cc_final: 0.6338 (p0) REVERT: A 103 TRP cc_start: 0.6385 (OUTLIER) cc_final: 0.6069 (p-90) REVERT: A 112 TRP cc_start: 0.7435 (m-10) cc_final: 0.7170 (m100) REVERT: B 73 SER cc_start: 0.7965 (p) cc_final: 0.7656 (t) REVERT: B 85 ASP cc_start: 0.7413 (m-30) cc_final: 0.7204 (m-30) REVERT: B 97 SER cc_start: 0.7521 (m) cc_final: 0.7245 (p) REVERT: B 102 PHE cc_start: 0.7074 (m-80) cc_final: 0.6773 (m-10) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.2115 time to fit residues: 19.8883 Evaluate side-chains 79 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5383 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3448 Z= 0.202 Angle : 0.565 4.800 4689 Z= 0.305 Chirality : 0.045 0.140 502 Planarity : 0.005 0.038 609 Dihedral : 4.216 17.633 481 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 0.27 % Allowed : 2.70 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.38), residues: 427 helix: -4.96 (0.74), residues: 7 sheet: -0.52 (0.43), residues: 138 loop : -2.95 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 103 HIS 0.001 0.001 HIS C 505 PHE 0.012 0.002 PHE C 342 TYR 0.025 0.002 TYR A 106 ARG 0.004 0.001 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 471 GLU cc_start: 0.7546 (pm20) cc_final: 0.6891 (pm20) REVERT: A 34 MET cc_start: 0.6373 (mmm) cc_final: 0.5431 (mmp) REVERT: A 67 ARG cc_start: 0.7269 (mtm110) cc_final: 0.6887 (mtm110) REVERT: B 37 TYR cc_start: 0.5638 (m-80) cc_final: 0.5172 (m-10) REVERT: B 73 SER cc_start: 0.7943 (p) cc_final: 0.7624 (t) REVERT: B 85 ASP cc_start: 0.7445 (m-30) cc_final: 0.7225 (m-30) REVERT: B 102 PHE cc_start: 0.7094 (m-80) cc_final: 0.6712 (m-10) REVERT: B 106 THR cc_start: 0.7701 (m) cc_final: 0.7231 (p) outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.2046 time to fit residues: 18.0960 Evaluate side-chains 74 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN A 77 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5458 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3448 Z= 0.215 Angle : 0.594 7.381 4689 Z= 0.318 Chirality : 0.045 0.132 502 Planarity : 0.004 0.037 609 Dihedral : 4.626 18.947 481 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer: Outliers : 0.27 % Allowed : 4.05 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.39), residues: 427 helix: -4.82 (0.88), residues: 7 sheet: -0.64 (0.44), residues: 134 loop : -2.83 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 103 HIS 0.003 0.001 HIS C 505 PHE 0.013 0.002 PHE B 102 TYR 0.022 0.002 TYR A 106 ARG 0.004 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 457 ARG cc_start: 0.6966 (tpp80) cc_final: 0.5511 (ttp80) REVERT: C 471 GLU cc_start: 0.7677 (pm20) cc_final: 0.6988 (pm20) REVERT: A 34 MET cc_start: 0.6396 (mmm) cc_final: 0.5844 (mmm) REVERT: A 36 TRP cc_start: 0.6786 (m100) cc_final: 0.6501 (m100) REVERT: A 39 GLN cc_start: 0.7495 (tt0) cc_final: 0.7257 (tt0) REVERT: A 45 LEU cc_start: 0.8249 (mt) cc_final: 0.8016 (mt) REVERT: A 67 ARG cc_start: 0.7199 (mtm110) cc_final: 0.6773 (mtp180) REVERT: A 96 CYS cc_start: 0.3919 (p) cc_final: 0.3373 (p) REVERT: B 37 TYR cc_start: 0.5514 (m-80) cc_final: 0.5243 (m-10) REVERT: B 73 SER cc_start: 0.7984 (p) cc_final: 0.7684 (t) REVERT: B 102 PHE cc_start: 0.6949 (m-80) cc_final: 0.6739 (m-10) outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 0.1944 time to fit residues: 18.0684 Evaluate side-chains 71 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.0060 chunk 8 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3448 Z= 0.181 Angle : 0.566 4.304 4689 Z= 0.306 Chirality : 0.045 0.130 502 Planarity : 0.004 0.037 609 Dihedral : 4.523 19.803 481 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 0.27 % Allowed : 2.70 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.38), residues: 427 helix: -4.29 (1.40), residues: 7 sheet: -0.61 (0.44), residues: 131 loop : -2.85 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 103 HIS 0.002 0.001 HIS B 99 PHE 0.010 0.001 PHE B 102 TYR 0.018 0.002 TYR B 37 ARG 0.003 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 346 ARG cc_start: 0.7001 (ptp90) cc_final: 0.6320 (ptp90) REVERT: C 452 LEU cc_start: 0.8357 (pp) cc_final: 0.8155 (pt) REVERT: C 471 GLU cc_start: 0.7614 (pm20) cc_final: 0.6922 (pm20) REVERT: C 494 SER cc_start: 0.7949 (p) cc_final: 0.7713 (p) REVERT: A 39 GLN cc_start: 0.7586 (tt0) cc_final: 0.7378 (tt0) REVERT: A 67 ARG cc_start: 0.7192 (mtm110) cc_final: 0.6835 (mtm110) REVERT: B 73 SER cc_start: 0.7962 (p) cc_final: 0.7689 (t) REVERT: B 102 PHE cc_start: 0.6839 (m-80) cc_final: 0.6603 (m-10) REVERT: B 106 THR cc_start: 0.7646 (m) cc_final: 0.7156 (p) outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 0.2266 time to fit residues: 19.2290 Evaluate side-chains 70 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 overall best weight: 0.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5488 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3448 Z= 0.244 Angle : 0.626 5.402 4689 Z= 0.333 Chirality : 0.046 0.135 502 Planarity : 0.005 0.037 609 Dihedral : 4.876 20.847 481 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.39), residues: 427 helix: -3.82 (1.15), residues: 13 sheet: -0.40 (0.46), residues: 127 loop : -2.89 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 112 HIS 0.002 0.001 HIS B 99 PHE 0.009 0.001 PHE C 342 TYR 0.017 0.002 TYR A 106 ARG 0.005 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 358 ILE cc_start: 0.6163 (mt) cc_final: 0.5690 (mm) REVERT: C 457 ARG cc_start: 0.7187 (tpp-160) cc_final: 0.5713 (ttp80) REVERT: C 466 ARG cc_start: 0.3645 (mtp-110) cc_final: 0.3429 (mpt90) REVERT: C 471 GLU cc_start: 0.7574 (pm20) cc_final: 0.6887 (pm20) REVERT: C 494 SER cc_start: 0.7875 (p) cc_final: 0.7603 (p) REVERT: A 36 TRP cc_start: 0.6637 (m100) cc_final: 0.6345 (m100) REVERT: A 39 GLN cc_start: 0.7602 (tt0) cc_final: 0.7274 (tt0) REVERT: A 67 ARG cc_start: 0.7259 (mtm110) cc_final: 0.6871 (mtm110) REVERT: B 36 TRP cc_start: 0.6657 (m100) cc_final: 0.6244 (m100) REVERT: B 81 LEU cc_start: 0.8036 (tp) cc_final: 0.7615 (tp) REVERT: B 100 VAL cc_start: 0.8646 (t) cc_final: 0.8414 (t) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2329 time to fit residues: 20.6770 Evaluate side-chains 71 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5497 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3448 Z= 0.236 Angle : 0.646 7.679 4689 Z= 0.344 Chirality : 0.046 0.135 502 Planarity : 0.005 0.037 609 Dihedral : 5.086 22.055 481 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.39), residues: 427 helix: -4.05 (1.03), residues: 15 sheet: -0.55 (0.46), residues: 128 loop : -2.92 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP A 112 HIS 0.004 0.001 HIS B 99 PHE 0.017 0.002 PHE C 347 TYR 0.018 0.002 TYR A 106 ARG 0.004 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 358 ILE cc_start: 0.6102 (mt) cc_final: 0.5896 (mt) REVERT: C 452 LEU cc_start: 0.8396 (pp) cc_final: 0.8187 (pt) REVERT: C 457 ARG cc_start: 0.7167 (tpp-160) cc_final: 0.5833 (ttp80) REVERT: C 466 ARG cc_start: 0.3817 (mtp-110) cc_final: 0.3261 (mpt90) REVERT: C 471 GLU cc_start: 0.7586 (pm20) cc_final: 0.6975 (pm20) REVERT: A 36 TRP cc_start: 0.6637 (m100) cc_final: 0.6405 (m100) REVERT: A 39 GLN cc_start: 0.7518 (tt0) cc_final: 0.7259 (tt0) REVERT: A 67 ARG cc_start: 0.7175 (mtm110) cc_final: 0.6775 (mtm110) REVERT: B 62 ARG cc_start: 0.8034 (mmm160) cc_final: 0.7758 (mmm160) REVERT: B 81 LEU cc_start: 0.8008 (tp) cc_final: 0.7594 (tp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2372 time to fit residues: 19.4146 Evaluate side-chains 65 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.0060 chunk 36 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3448 Z= 0.160 Angle : 0.575 5.228 4689 Z= 0.305 Chirality : 0.045 0.139 502 Planarity : 0.005 0.038 609 Dihedral : 4.663 21.469 481 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.39), residues: 427 helix: -3.57 (1.33), residues: 13 sheet: -0.38 (0.46), residues: 130 loop : -2.90 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 47 HIS 0.003 0.001 HIS B 99 PHE 0.012 0.001 PHE C 347 TYR 0.034 0.001 TYR A 106 ARG 0.007 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 346 ARG cc_start: 0.7090 (ptp90) cc_final: 0.6874 (ptp90) REVERT: C 452 LEU cc_start: 0.8460 (pp) cc_final: 0.8248 (pt) REVERT: C 457 ARG cc_start: 0.7326 (tpp-160) cc_final: 0.5870 (ttp80) REVERT: C 466 ARG cc_start: 0.3613 (mtp-110) cc_final: 0.3252 (mpt90) REVERT: C 471 GLU cc_start: 0.7453 (pm20) cc_final: 0.6857 (pm20) REVERT: C 494 SER cc_start: 0.7829 (p) cc_final: 0.7584 (p) REVERT: A 45 LEU cc_start: 0.8308 (mt) cc_final: 0.7732 (mt) REVERT: A 67 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6741 (mtm110) REVERT: B 106 THR cc_start: 0.7525 (m) cc_final: 0.7012 (p) REVERT: B 107 LYS cc_start: 0.7335 (ttpp) cc_final: 0.6928 (ttpp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2341 time to fit residues: 19.3462 Evaluate side-chains 70 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0030 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.0270 chunk 39 optimal weight: 0.5980 chunk 18 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5377 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3448 Z= 0.144 Angle : 0.563 5.811 4689 Z= 0.298 Chirality : 0.045 0.138 502 Planarity : 0.004 0.041 609 Dihedral : 4.507 20.674 481 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.65 % Favored : 87.35 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.39), residues: 427 helix: -3.63 (1.26), residues: 13 sheet: -0.36 (0.47), residues: 129 loop : -2.86 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 103 HIS 0.002 0.001 HIS B 99 PHE 0.010 0.001 PHE C 347 TYR 0.023 0.001 TYR A 106 ARG 0.007 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 346 ARG cc_start: 0.7130 (ptp90) cc_final: 0.6906 (ptp90) REVERT: C 452 LEU cc_start: 0.8464 (pp) cc_final: 0.8252 (pt) REVERT: C 457 ARG cc_start: 0.7228 (tpp-160) cc_final: 0.5791 (ttp80) REVERT: C 471 GLU cc_start: 0.7432 (pm20) cc_final: 0.6825 (pm20) REVERT: C 494 SER cc_start: 0.7852 (p) cc_final: 0.7618 (p) REVERT: A 36 TRP cc_start: 0.6543 (m100) cc_final: 0.6308 (m100) REVERT: A 67 ARG cc_start: 0.7181 (mtm110) cc_final: 0.6890 (mtm110) REVERT: B 81 LEU cc_start: 0.8013 (tp) cc_final: 0.7567 (tp) REVERT: B 106 THR cc_start: 0.7611 (m) cc_final: 0.7088 (p) REVERT: B 107 LYS cc_start: 0.7318 (ttpp) cc_final: 0.6889 (ttpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2315 time to fit residues: 19.5262 Evaluate side-chains 70 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 10 optimal weight: 0.0370 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN B 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5431 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3448 Z= 0.167 Angle : 0.579 6.045 4689 Z= 0.307 Chirality : 0.045 0.137 502 Planarity : 0.005 0.045 609 Dihedral : 4.647 21.352 481 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.40), residues: 427 helix: -3.90 (1.06), residues: 15 sheet: -0.35 (0.47), residues: 125 loop : -2.69 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 103 HIS 0.002 0.001 HIS B 99 PHE 0.009 0.001 PHE C 347 TYR 0.029 0.001 TYR A 106 ARG 0.008 0.001 ARG A 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 346 ARG cc_start: 0.7166 (ptp90) cc_final: 0.6930 (ptp90) REVERT: C 452 LEU cc_start: 0.8478 (pp) cc_final: 0.8264 (pt) REVERT: C 457 ARG cc_start: 0.7170 (tpp-160) cc_final: 0.5627 (ttp80) REVERT: C 466 ARG cc_start: 0.3816 (mpt90) cc_final: 0.3333 (mpt90) REVERT: C 471 GLU cc_start: 0.7441 (pm20) cc_final: 0.6819 (pm20) REVERT: C 494 SER cc_start: 0.7726 (p) cc_final: 0.7479 (p) REVERT: A 67 ARG cc_start: 0.7396 (mtm110) cc_final: 0.7049 (mtm110) REVERT: B 73 SER cc_start: 0.8003 (p) cc_final: 0.7737 (t) REVERT: B 81 LEU cc_start: 0.8010 (tp) cc_final: 0.7624 (tp) REVERT: B 106 THR cc_start: 0.7587 (m) cc_final: 0.7048 (p) REVERT: B 107 LYS cc_start: 0.7389 (ttpp) cc_final: 0.6954 (ttpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2192 time to fit residues: 19.3653 Evaluate side-chains 74 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.0000 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.193835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.170589 restraints weight = 7664.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.175508 restraints weight = 5020.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.178916 restraints weight = 3567.150| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3448 Z= 0.187 Angle : 0.610 6.277 4689 Z= 0.322 Chirality : 0.045 0.139 502 Planarity : 0.005 0.044 609 Dihedral : 4.814 20.941 481 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.40), residues: 427 helix: -3.88 (1.08), residues: 15 sheet: -0.35 (0.46), residues: 129 loop : -2.69 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.005 TRP A 36 HIS 0.002 0.001 HIS B 99 PHE 0.010 0.001 PHE C 347 TYR 0.030 0.002 TYR A 106 ARG 0.006 0.001 ARG C 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1317.43 seconds wall clock time: 24 minutes 1.22 seconds (1441.22 seconds total)