Starting phenix.real_space_refine on Sun Mar 10 16:56:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wog_32651/03_2024/7wog_32651.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wog_32651/03_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_32651/03_2024/7wog_32651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wog_32651/03_2024/7wog_32651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wog_32651/03_2024/7wog_32651.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wog_32651/03_2024/7wog_32651.pdb" } 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 Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 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: 2.68, per 1000 atoms: 0.80 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 - 3.50 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: 1.48 Conformation dependent library (CDL) restraints added in 724.0 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: 0.54 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: 0.81 Time building geometry restraints manager: 1.61 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: 100.87 - 107.49: 123 107.49 - 114.11: 1858 114.11 - 120.72: 1307 120.72 - 127.34: 1367 127.34 - 133.95: 34 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 2.440 nonbonded pdb=" O TRP C 353 " pdb=" OH TYR A 106 " model vdw 2.316 2.440 nonbonded pdb=" O SER A 31 " pdb=" OG SER A 102 " model vdw 2.343 2.440 nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.352 2.440 nonbonded pdb=" NH1 ARG A 67 " pdb=" O SER A 85 " model vdw 2.360 2.520 ... (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 ========== 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: 0.970 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: 2.950 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.230 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- 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: 0.2446 time to fit residues: 27.4104 Evaluate side-chains 86 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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: 0.0870 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.0070 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 448 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5250 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3448 Z= 0.175 Angle : 0.546 5.986 4689 Z= 0.294 Chirality : 0.044 0.184 502 Planarity : 0.005 0.035 609 Dihedral : 3.891 20.702 481 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.32 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: -3.22 (0.37), residues: 427 helix: -5.17 (0.50), residues: 7 sheet: -0.26 (0.44), residues: 117 loop : -3.11 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 103 HIS 0.001 0.000 HIS C 505 PHE 0.016 0.002 PHE C 347 TYR 0.020 0.002 TYR A 106 ARG 0.004 0.001 ARG C 466 *********************** 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 85 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 338 PHE cc_start: 0.6684 (m-10) cc_final: 0.6471 (m-10) REVERT: C 408 ARG cc_start: 0.6872 (ptm-80) cc_final: 0.5353 (mmm-85) REVERT: C 452 LEU cc_start: 0.8343 (pp) cc_final: 0.8093 (pt) REVERT: C 457 ARG cc_start: 0.6588 (tpp80) cc_final: 0.6075 (tpp80) REVERT: C 471 GLU cc_start: 0.7098 (pm20) cc_final: 0.6717 (pm20) REVERT: A 34 MET cc_start: 0.6648 (mmm) cc_final: 0.6101 (mmm) REVERT: A 51 ILE cc_start: 0.7488 (tt) cc_final: 0.7251 (tt) REVERT: A 77 ASN cc_start: 0.6508 (p0) cc_final: 0.6208 (p0) REVERT: A 112 TRP cc_start: 0.7196 (m-10) cc_final: 0.6838 (m100) REVERT: B 73 SER cc_start: 0.7989 (p) cc_final: 0.7578 (t) REVERT: B 97 SER cc_start: 0.7524 (m) cc_final: 0.7304 (p) REVERT: B 102 PHE cc_start: 0.6821 (m-80) cc_final: 0.6512 (m-10) REVERT: B 106 THR cc_start: 0.7653 (m) cc_final: 0.7265 (p) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1970 time to fit residues: 19.6453 Evaluate side-chains 79 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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: 0.6980 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.0070 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN C 422 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5362 moved from start: 0.3442 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= 0.184 Angle : 0.529 4.307 4689 Z= 0.285 Chirality : 0.044 0.244 502 Planarity : 0.004 0.031 609 Dihedral : 3.975 19.272 481 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.71 % Favored : 88.29 % Rotamer: Outliers : 0.27 % Allowed : 3.78 % Favored : 95.95 % 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: -2.91 (0.38), residues: 427 helix: -4.79 (0.90), residues: 7 sheet: -0.08 (0.45), residues: 125 loop : -2.95 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 103 HIS 0.001 0.000 HIS C 505 PHE 0.010 0.001 PHE C 377 TYR 0.025 0.002 TYR A 106 ARG 0.004 0.001 ARG C 457 *********************** 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 80 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 452 LEU cc_start: 0.8303 (pp) cc_final: 0.8030 (pt) REVERT: C 471 GLU cc_start: 0.7154 (pm20) cc_final: 0.6752 (pm20) REVERT: A 34 MET cc_start: 0.6439 (mmm) cc_final: 0.5449 (mmp) REVERT: A 77 ASN cc_start: 0.6463 (p0) cc_final: 0.6241 (p0) REVERT: B 73 SER cc_start: 0.7992 (p) cc_final: 0.7611 (t) REVERT: B 81 LEU cc_start: 0.7888 (tp) cc_final: 0.7537 (tp) REVERT: B 85 ASP cc_start: 0.7375 (m-30) cc_final: 0.7138 (m-30) REVERT: B 106 THR cc_start: 0.7737 (m) cc_final: 0.7332 (p) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.2100 time to fit residues: 19.1971 Evaluate side-chains 71 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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: 0.7980 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5448 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3448 Z= 0.231 Angle : 0.583 5.322 4689 Z= 0.311 Chirality : 0.044 0.126 502 Planarity : 0.005 0.032 609 Dihedral : 4.596 19.632 481 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 0.00 % Allowed : 4.32 % 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: -2.97 (0.38), residues: 427 helix: -4.70 (0.52), residues: 15 sheet: -0.23 (0.45), residues: 125 loop : -2.85 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 103 HIS 0.003 0.001 HIS B 99 PHE 0.010 0.001 PHE C 464 TYR 0.025 0.002 TYR A 106 ARG 0.004 0.001 ARG C 457 *********************** 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 77 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.6413 (mmm) cc_final: 0.5894 (mmm) REVERT: A 39 GLN cc_start: 0.7364 (tp40) cc_final: 0.6962 (tp40) REVERT: B 73 SER cc_start: 0.8014 (p) cc_final: 0.7724 (t) REVERT: B 81 LEU cc_start: 0.7956 (tp) cc_final: 0.7631 (tp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1999 time to fit residues: 18.1983 Evaluate side-chains 73 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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: 0.8980 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.0020 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.0570 overall best weight: 0.3706 ------------------------------------------------------------------------------- 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: 0.5394 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3448 Z= 0.151 Angle : 0.542 5.204 4689 Z= 0.288 Chirality : 0.044 0.133 502 Planarity : 0.004 0.032 609 Dihedral : 4.338 18.403 481 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % 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: -3.05 (0.38), residues: 427 helix: -4.53 (0.63), residues: 15 sheet: -0.39 (0.45), residues: 133 loop : -2.92 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 103 HIS 0.001 0.000 HIS B 99 PHE 0.008 0.001 PHE C 342 TYR 0.020 0.001 TYR A 106 ARG 0.002 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 75 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 457 ARG cc_start: 0.7142 (tpp80) cc_final: 0.6590 (tpp-160) REVERT: C 494 SER cc_start: 0.7882 (p) cc_final: 0.7655 (p) REVERT: A 34 MET cc_start: 0.6292 (mmm) cc_final: 0.5512 (mmp) REVERT: A 36 TRP cc_start: 0.6620 (m100) cc_final: 0.6255 (m100) REVERT: A 39 GLN cc_start: 0.7367 (tp40) cc_final: 0.6914 (tp40) REVERT: A 103 TRP cc_start: 0.6735 (p-90) cc_final: 0.6427 (p-90) REVERT: B 73 SER cc_start: 0.7955 (p) cc_final: 0.7662 (t) REVERT: B 81 LEU cc_start: 0.7983 (tp) cc_final: 0.7627 (tp) REVERT: B 94 TYR cc_start: 0.6756 (m-80) cc_final: 0.6504 (m-80) REVERT: B 106 THR cc_start: 0.7672 (m) cc_final: 0.7224 (p) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1968 time to fit residues: 17.4566 Evaluate side-chains 73 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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: 0.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 0.5008 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= 0.221 Angle : 0.594 4.625 4689 Z= 0.319 Chirality : 0.044 0.135 502 Planarity : 0.004 0.032 609 Dihedral : 4.843 21.323 481 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % 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: -2.81 (0.39), residues: 427 helix: -4.70 (0.52), residues: 15 sheet: -0.06 (0.47), residues: 122 loop : -2.74 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 103 HIS 0.003 0.001 HIS B 99 PHE 0.009 0.001 PHE B 102 TYR 0.025 0.002 TYR A 106 ARG 0.005 0.001 ARG C 346 *********************** 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 76 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 457 ARG cc_start: 0.7115 (tpp80) cc_final: 0.6477 (tpp-160) REVERT: C 493 ARG cc_start: 0.5297 (ptp-170) cc_final: 0.5051 (ptt180) REVERT: C 494 SER cc_start: 0.7820 (p) cc_final: 0.7597 (p) REVERT: A 34 MET cc_start: 0.6392 (mmm) cc_final: 0.5640 (mmp) REVERT: A 36 TRP cc_start: 0.6770 (m100) cc_final: 0.6406 (m100) REVERT: A 39 GLN cc_start: 0.7410 (tp40) cc_final: 0.7034 (tp-100) REVERT: B 73 SER cc_start: 0.7984 (p) cc_final: 0.7761 (t) REVERT: B 81 LEU cc_start: 0.7952 (tp) cc_final: 0.7609 (tp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2133 time to fit residues: 18.9982 Evaluate side-chains 68 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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: 0.7980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN C 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5496 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3448 Z= 0.234 Angle : 0.630 6.350 4689 Z= 0.336 Chirality : 0.045 0.136 502 Planarity : 0.005 0.046 609 Dihedral : 5.075 20.785 481 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: -2.87 (0.39), residues: 427 helix: -4.75 (0.51), residues: 15 sheet: -0.19 (0.47), residues: 122 loop : -2.73 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 47 HIS 0.004 0.001 HIS B 99 PHE 0.012 0.002 PHE A 29 TYR 0.040 0.002 TYR A 106 ARG 0.006 0.001 ARG C 346 *********************** 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 75 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 457 ARG cc_start: 0.7227 (tpp80) cc_final: 0.6828 (tpp-160) REVERT: C 494 SER cc_start: 0.7812 (p) cc_final: 0.7583 (p) REVERT: A 36 TRP cc_start: 0.6800 (m100) cc_final: 0.6351 (m100) REVERT: A 39 GLN cc_start: 0.7342 (tp40) cc_final: 0.6772 (tp40) REVERT: A 45 LEU cc_start: 0.8262 (mt) cc_final: 0.7973 (mt) REVERT: A 47 TRP cc_start: 0.8424 (t60) cc_final: 0.8207 (t60) REVERT: A 96 CYS cc_start: 0.3896 (p) cc_final: 0.3571 (p) REVERT: B 81 LEU cc_start: 0.7927 (tp) cc_final: 0.7592 (tp) REVERT: B 100 VAL cc_start: 0.8691 (t) cc_final: 0.8359 (t) REVERT: B 106 THR cc_start: 0.7543 (m) cc_final: 0.7044 (p) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2038 time to fit residues: 18.0190 Evaluate side-chains 68 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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: 0.4980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 0.0050 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.0770 chunk 34 optimal weight: 0.5980 overall best weight: 0.3752 ------------------------------------------------------------------------------- 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: 0.5420 moved from start: 0.5452 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= 0.150 Angle : 0.572 6.109 4689 Z= 0.303 Chirality : 0.044 0.136 502 Planarity : 0.004 0.038 609 Dihedral : 4.681 21.309 481 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: -2.74 (0.40), residues: 427 helix: -4.42 (0.68), residues: 15 sheet: -0.20 (0.48), residues: 121 loop : -2.59 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 103 HIS 0.001 0.000 HIS B 99 PHE 0.007 0.001 PHE A 29 TYR 0.024 0.001 TYR A 106 ARG 0.005 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 73 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 457 ARG cc_start: 0.7227 (tpp80) cc_final: 0.6877 (tpp-160) REVERT: C 466 ARG cc_start: 0.3777 (mtp180) cc_final: 0.3376 (mpt90) REVERT: A 34 MET cc_start: 0.6415 (mmm) cc_final: 0.5704 (mmp) REVERT: A 36 TRP cc_start: 0.6649 (m100) cc_final: 0.6409 (m100) REVERT: A 39 GLN cc_start: 0.7400 (tp40) cc_final: 0.6899 (tp40) REVERT: A 45 LEU cc_start: 0.8192 (mt) cc_final: 0.7919 (mt) REVERT: B 36 TRP cc_start: 0.6738 (m100) cc_final: 0.6238 (m-10) REVERT: B 73 SER cc_start: 0.7986 (p) cc_final: 0.7709 (t) REVERT: B 76 LEU cc_start: 0.7800 (tp) cc_final: 0.6790 (tp) REVERT: B 81 LEU cc_start: 0.7930 (tp) cc_final: 0.7608 (tp) REVERT: B 106 THR cc_start: 0.7552 (m) cc_final: 0.7077 (p) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2180 time to fit residues: 18.5267 Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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: 0.6980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.0970 chunk 18 optimal weight: 0.0030 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5411 moved from start: 0.5534 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= 0.145 Angle : 0.571 5.585 4689 Z= 0.302 Chirality : 0.044 0.134 502 Planarity : 0.004 0.040 609 Dihedral : 4.652 22.001 481 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: -2.63 (0.40), residues: 427 helix: -4.29 (0.73), residues: 15 sheet: -0.15 (0.48), residues: 121 loop : -2.50 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 103 HIS 0.002 0.000 HIS B 99 PHE 0.007 0.001 PHE B 102 TYR 0.024 0.001 TYR A 106 ARG 0.011 0.001 ARG A 19 *********************** 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 72 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 457 ARG cc_start: 0.7130 (tpp80) cc_final: 0.6873 (tpp-160) REVERT: C 466 ARG cc_start: 0.3754 (mtp180) cc_final: 0.3332 (mpt90) REVERT: C 494 SER cc_start: 0.7669 (p) cc_final: 0.7425 (p) REVERT: A 34 MET cc_start: 0.6309 (mmm) cc_final: 0.5531 (mmp) REVERT: A 36 TRP cc_start: 0.6672 (m100) cc_final: 0.6408 (m100) REVERT: A 39 GLN cc_start: 0.7345 (tp40) cc_final: 0.6968 (tp40) REVERT: A 45 LEU cc_start: 0.8213 (mt) cc_final: 0.7977 (mt) REVERT: B 73 SER cc_start: 0.7941 (p) cc_final: 0.7694 (t) REVERT: B 81 LEU cc_start: 0.8007 (tp) cc_final: 0.7670 (tp) REVERT: B 106 THR cc_start: 0.7582 (m) cc_final: 0.7099 (p) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1895 time to fit residues: 16.2134 Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3448 Z= 0.196 Angle : 0.610 5.033 4689 Z= 0.321 Chirality : 0.045 0.133 502 Planarity : 0.005 0.042 609 Dihedral : 4.967 23.664 481 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 20.90 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: -2.66 (0.40), residues: 427 helix: -4.05 (0.89), residues: 14 sheet: -0.18 (0.49), residues: 120 loop : -2.54 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 103 HIS 0.002 0.001 HIS B 99 PHE 0.007 0.001 PHE A 68 TYR 0.026 0.002 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 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 494 SER cc_start: 0.7803 (p) cc_final: 0.7553 (p) REVERT: A 34 MET cc_start: 0.6391 (mmm) cc_final: 0.5724 (mmp) REVERT: A 36 TRP cc_start: 0.6765 (m100) cc_final: 0.6388 (m100) REVERT: A 39 GLN cc_start: 0.7336 (tp40) cc_final: 0.6903 (tp40) REVERT: A 45 LEU cc_start: 0.8311 (mt) cc_final: 0.8037 (mt) REVERT: B 81 LEU cc_start: 0.8067 (tp) cc_final: 0.7704 (tp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1746 time to fit residues: 14.5178 Evaluate side-chains 65 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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: 0.0870 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.0050 chunk 41 optimal weight: 2.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN ** A 82 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 = 0.4527 r_free = 0.4527 target = 0.194828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.171414 restraints weight = 7724.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.176258 restraints weight = 5015.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.179628 restraints weight = 3556.517| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5466 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3448 Z= 0.167 Angle : 0.624 7.532 4689 Z= 0.324 Chirality : 0.045 0.140 502 Planarity : 0.005 0.042 609 Dihedral : 4.849 22.073 481 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % 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: -2.57 (0.41), residues: 427 helix: -3.75 (1.04), residues: 14 sheet: -0.18 (0.49), residues: 121 loop : -2.47 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 103 HIS 0.002 0.001 HIS B 99 PHE 0.008 0.001 PHE B 102 TYR 0.035 0.002 TYR B 37 ARG 0.008 0.001 ARG A 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1328.69 seconds wall clock time: 24 minutes 30.49 seconds (1470.49 seconds total)